4KWS | pdb_00004kws

Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg and glycerol

PDB DOI: https://doi.org/10.2210/pdb4KWS/pdb

Classification: HYDROLASE
Organism(s): Chromohalobacter israelensis DSM 3043
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-24 Released: 2014-05-28
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: 1.64 Å
R-Value Free:
0.163 (Depositor), 0.160 (DCC)
R-Value Work:
0.139 (Depositor), 0.140 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg and glycerol

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

To be published.

Macromolecule Content

Total Structure Weight: 364.94 kDa
Atom Count: 28,246
Modeled Residue Count: 3,164
Deposited Residue Count: 3,240
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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): 0 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 salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)) Explore Q1QT89 Go to UniProtKB: Q1QT89
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1QT89
Sequence Annotations Expand
Reference Sequence

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.163 (Depositor), 0.160 (DCC)
R-Value Work: 0.139 (Depositor), 0.140 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.273	α = 90
b = 85.762	β = 110.31
c = 195.097	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description