8F9X

Cyclase-Phosphotriesterase from Ruegeria pomeroyi DSS-3

PDB DOI: https://doi.org/10.2210/pdb8F9X/pdb

Classification: HYDROLASE
Organism(s): Ruegeria pomeroyi DSS-3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-24 Released: 2023-12-06
Deposition Author(s): Frkic, R.L., Ji, D., Jackson, C.J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.253 (Depositor), 0.249 (DCC)
R-Value Work:
0.219 (Depositor), 0.216 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Cyclase-PTE

Ji, D., Frkic, R.L., Jackson, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 249.33 kDa
Atom Count: 17,432
Modelled Residue Count: 2,274
Deposited Residue Count: 2,300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclase family protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	230	Ruegeria pomeroyi DSS-3	Mutation(s): 0 Gene Names: SPO0761
UniProt
Find proteins for Q5LVE1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LVE1 Go to UniProtKB: Q5LVE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LVE1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain EB [auth H] SDF format, chain FA [auth D] SDF format, chain M [auth A] SDF format, chain MB [auth I] SDF format, chain N [auth A] SDF format, chain PA [auth F] SDF format, chain PB [auth I] SDF format, chain QA [auth F] SDF format, chain U [auth B] SDF format, chain UB [auth J] SDF format, chain VB [auth J] SDF format, chain X [auth C] SDF format, chain XA [auth G] SDF format, chain YA [auth G] MOL2 format, chain EB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain PB [auth I] MOL2 format, chain QA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth J] MOL2 format, chain VB [auth J] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] mmCIF format, chain EB [auth H] mmCIF format, chain FA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth I] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain PB [auth I] mmCIF format, chain QA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain UB [auth J] mmCIF format, chain VB [auth J] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G]	EB [auth H] FA [auth D] M [auth A] MB [auth I] N [auth A] EB [auth H], FA [auth D], M [auth A], MB [auth I], N [auth A], PA [auth F], PB [auth I], QA [auth F], U [auth B], UB [auth J], VB [auth J], X [auth C], XA [auth G], YA [auth G]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain EB [auth H] Focus chain FA [auth D] Focus chain M [auth A] Focus chain MB [auth I] Focus chain N [auth A] Focus chain PA [auth F] Focus chain PB [auth I] Focus chain QA [auth F] Focus chain U [auth B] Focus chain UB [auth J] Focus chain VB [auth J] Focus chain X [auth C] Focus chain XA [auth G] Focus chain YA [auth G] Interactions & Density Focus chain EB [auth H] Focus chain FA [auth D] Focus chain M [auth A] Focus chain MB [auth I] Focus chain N [auth A] Focus chain PA [auth F] Focus chain PB [auth I] Focus chain QA [auth F] Focus chain U [auth B] Focus chain UB [auth J] Focus chain VB [auth J] Focus chain X [auth C] Focus chain XA [auth G] Focus chain YA [auth G]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain BA [auth C]	BA [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Interactions & Density Focus chain BA [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain JA [auth E] SDF format, chain LB [auth I] SDF format, chain T [auth B] SDF format, chain TB [auth J] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain LB [auth I] MOL2 format, chain T [auth B] MOL2 format, chain TB [auth J] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain LB [auth I] mmCIF format, chain T [auth B] mmCIF format, chain TB [auth J]	DB [auth H] EA [auth D] JA [auth E] LB [auth I] T [auth B] DB [auth H], EA [auth D], JA [auth E], LB [auth I], T [auth B], TB [auth J]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain DB [auth H] Focus chain EA [auth D] Focus chain JA [auth E] Focus chain LB [auth I] Focus chain T [auth B] Focus chain TB [auth J] Interactions & Density Focus chain DB [auth H] Focus chain EA [auth D] Focus chain JA [auth E] Focus chain LB [auth I] Focus chain T [auth B] Focus chain TB [auth J]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BB [auth H] SDF format, chain CA [auth D] SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain IB [auth I] SDF format, chain JB [auth I] SDF format, chain K [auth A] SDF format, chain KB [auth I] SDF format, chain L [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain Q [auth B] SDF format, chain QB [auth J] SDF format, chain R [auth B] SDF format, chain RB [auth J] SDF format, chain S [auth B] SDF format, chain SB [auth J] SDF format, chain UA [auth G] SDF format, chain V [auth C] SDF format, chain VA [auth G] SDF format, chain W [auth C] SDF format, chain WA [auth G] MOL2 format, chain AB [auth H] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth I] MOL2 format, chain JB [auth I] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth I] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QB [auth J] MOL2 format, chain R [auth B] MOL2 format, chain RB [auth J] MOL2 format, chain S [auth B] MOL2 format, chain SB [auth J] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] mmCIF format, chain AB [auth H] mmCIF format, chain BB [auth H] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth I] mmCIF format, chain JB [auth I] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth I] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QB [auth J] mmCIF format, chain R [auth B] mmCIF format, chain RB [auth J] mmCIF format, chain S [auth B] mmCIF format, chain SB [auth J] mmCIF format, chain UA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth G]	AB [auth H] BB [auth H] CA [auth D] CB [auth H] DA [auth D] AB [auth H], BB [auth H], CA [auth D], CB [auth H], DA [auth D], HA [auth E], IA [auth E], IB [auth I], JB [auth I], K [auth A], KB [auth I], L [auth A], NA [auth F], OA [auth F], Q [auth B], QB [auth J], R [auth B], RB [auth J], S [auth B], SB [auth J], UA [auth G], V [auth C], VA [auth G], W [auth C], WA [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain K [auth A] Focus chain KB [auth I] Focus chain L [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RB [auth J] Focus chain S [auth B] Focus chain SB [auth J] Focus chain UA [auth G] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Interactions & Density Focus chain AB [auth H] Focus chain BB [auth H] Focus chain CA [auth D] Focus chain CB [auth H] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain K [auth A] Focus chain KB [auth I] Focus chain L [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain Q [auth B] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RB [auth J] Focus chain S [auth B] Focus chain SB [auth J] Focus chain UA [auth G] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FB [auth H] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain HB [auth H] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain NB [auth I] SDF format, chain O [auth A] SDF format, chain OB [auth I] SDF format, chain P [auth A] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain TA [auth F] SDF format, chain WB [auth J] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain ZA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain FB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain HB [auth H] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain NB [auth I] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth I] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain WB [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth G] mmCIF format, chain AA [auth C] mmCIF format, chain FB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain HB [auth H] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain NB [auth I] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth I] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth F] mmCIF format, chain SA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain WB [auth J] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth G]	AA [auth C] FB [auth H] GA [auth D] GB [auth H] HB [auth H] AA [auth C], FB [auth H], GA [auth D], GB [auth H], HB [auth H], KA [auth E], LA [auth E], MA [auth E], NB [auth I], O [auth A], OB [auth I], P [auth A], RA [auth F], SA [auth F], TA [auth F], WB [auth J], Y [auth C], Z [auth C], ZA [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NB [auth I] Focus chain O [auth A] Focus chain OB [auth I] Focus chain P [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain WB [auth J] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HB [auth H] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NB [auth I] Focus chain O [auth A] Focus chain OB [auth I] Focus chain P [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain TA [auth F] Focus chain WB [auth J] Focus chain Y [auth C] Focus chain Z [auth C] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.253 (Depositor), 0.249 (DCC)
R-Value Work: 0.219 (Depositor), 0.216 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.08	α = 90
b = 68.08	β = 90
c = 446.501	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

Frkic, R.L.

Ji, D.

Jackson, C.J.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE200100012
Australian Research Council (ARC)	Australia	CE200100029

Revision History (Full details and data files)

Version 1.0: 2023-12-06
Type: Initial release
Version 2.0: 2025-01-29
Type: Coordinate replacement
Reason: Atomic clashes
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary