2OX4

Crystal structure of putative dehydratase from Zymomonas mobilis ZM4

PDB DOI: https://doi.org/10.2210/pdb2OX4/pdb

Classification: ISOMERASE
Organism(s): Zymomonas mobilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-02-19 Released: 2007-03-06
Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Freeman, J.C., Bain, K., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.144 (Depositor), 0.140 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Putative Dehydratase from Zymomonas Mobilis Zm4

Patskovsky, Y., Toro, R., Sauder, J.M., Freeman, J.C., Bain, K., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 359.9 kDa
Atom Count: 28,439
Modelled Residue Count: 3,152
Deposited Residue Count: 3,224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative mandelate racemase	A, B, C, D, E A, B, C, D, E, F, G, H	403	Zymomonas mobilis	Mutation(s): 0 Gene Names: rspA, ZMO1264 EC: 5.1.2.2
UniProt
Find proteins for Q5NN22 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore Q5NN22 Go to UniProtKB: Q5NN22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NN22
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain HA [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	AA [auth F] DA [auth G] EA [auth G] FA [auth G] HA [auth H] AA [auth F], DA [auth G], EA [auth G], FA [auth G], HA [auth H], J [auth A], K [auth A], N [auth B], P [auth C], Q [auth C], T [auth D], U [auth D], W [auth E], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain Z [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain L [auth B] SDF format, chain S [auth D] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain L [auth B] mmCIF format, chain S [auth D] mmCIF format, chain Y [auth F]	BA [auth G], L [auth B], S [auth D], Y [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth G] Focus chain L [auth B] Focus chain S [auth D] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain L [auth B] Focus chain S [auth D] Focus chain Y [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain GA [auth H] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F]	CA [auth G] GA [auth H] I [auth A] M [auth B] O [auth C] CA [auth G], GA [auth H], I [auth A], M [auth B], O [auth C], R [auth D], V [auth E], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.144 (Depositor), 0.140 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.178	α = 90
b = 190.409	β = 90
c = 85.922	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-03-06

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-03-06
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2023-08-30
Changes: Data collection, Database references, Refinement description