4K2S | pdb_00004k2s

Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate

PDB DOI: https://doi.org/10.2210/pdb4K2S/pdb
Entry: 4K2S supersedes: 3QKF

Classification: ISOMERASE
Organism(s): Chromohalobacter israelensis DSM 3043
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-04-09 Released: 2014-04-09
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate

Fedorov, A.A., Fedorov, E.V., Wichelecki, D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 365.73 kDa
Atom Count: 28,312
Modeled Residue Count: 3,136
Deposited Residue Count: 3,240
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-mannonate dehydratase	A, B, C, D, E A, B, C, D, E, F, G, H	405	Chromohalobacter israelensis DSM 3043	Mutation(s): 1 Gene Names: Csal_2974 EC: 4.2.1.8 (PDB Primary Data), 4.2.1 (UniProt), 4.2.1.39 (UniProt)
UniProt
Find proteins for Q1QT89 (Chromohalobacter israelensis (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)) Explore Q1QT89 Go to UniProtKB: Q1QT89
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1QT89
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCO Query on GCO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain IA [auth H] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] SDF format, chain FA [auth G] SDF format, chain BA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] MOL2 format, chain FA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain W [auth E] mmCIF format, chain FA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] FA [auth G] I [auth A] IA [auth H] L [auth B] BA [auth F], FA [auth G], I [auth A], IA [auth H], L [auth B], O [auth C], S [auth D], W [auth E]	D-gluconic acid C₆ H₁₂ O₇ RGHNJXZEOKUKBD-SQOUGZDYSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G] Focus chain I [auth A] Focus chain IA [auth H] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain K [auth A] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	AA [auth E] DA [auth F] EA [auth F] K [auth A] V [auth D] AA [auth E], DA [auth F], EA [auth F], K [auth A], V [auth D], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain K [auth A] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain K [auth A] Focus chain V [auth D] Focus chain Z [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain J [auth A] SDF format, chain JA [auth H] SDF format, chain M [auth B] 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 X [auth E] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain M [auth B] 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 X [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain M [auth B] 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 X [auth E] mmCIF format, chain Y [auth E]	CA [auth F] GA [auth G] HA [auth G] J [auth A] JA [auth H] CA [auth F], GA [auth G], HA [auth G], J [auth A], JA [auth H], M [auth B], N [auth B], P [auth C], Q [auth C], T [auth D], U [auth D], X [auth E], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain J [auth A] Focus chain JA [auth H] Focus chain M [auth B] 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 X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain J [auth A] Focus chain JA [auth H] Focus chain M [auth B] 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 X [auth E] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203 (Depositor), 0.203 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.334	α = 90
b = 85.79	β = 110.47
c = 195.638	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-09

Deposition Author(s):

This entry supersedes: 3QKF

Revision History (Full details and data files)

Version 1.0: 2014-04-09
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary