6H2R | pdb_00006h2r

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant

PDB DOI: https://doi.org/10.2210/pdb6H2R/pdb

Classification: LYASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-07-16 Released: 2019-07-31
Deposition Author(s): Crennell, S.J., Danson, M.J., Royer, S.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.148 (Depositor), 0.148 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant

Crennell, S.J., Danson, M.J., Royer, S.

To be published.

Macromolecule Content

Total Structure Weight: 133.54 kDa
Atom Count: 11,325
Modeled Residue Count: 1,171
Deposited Residue Count: 1,172
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase	A, B, C, D	293	Saccharolobus solfataricus	Mutation(s): 3 EC: 4.1.2.55
UniProt
Find proteins for Q97U28 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97U28 Go to UniProtKB: Q97U28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97U28
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C]	K [auth B], O [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain K [auth B] Focus chain O [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	G [auth A], J [auth B], N [auth C], Q [auth D], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain S [auth D] mmCIF format, chain H [auth A] mmCIF format, chain S [auth D]	H [auth A], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain S [auth D]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	E [auth A] F [auth A] I [auth B] L [auth C] M [auth C] E [auth A], F [auth A], I [auth B], L [auth C], M [auth C], P [auth D]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.148 (Depositor), 0.148 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.352	α = 90
b = 86.906	β = 95.79
c = 91.982	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Crennell, S.J.

Danson, M.J.

Royer, S.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary