4KPL

Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg,d-mannonate and 2-keto-3-deoxy-d-gluconate

PDB DOI: https://doi.org/10.2210/pdb4KPL/pdb

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

Deposited: 2013-05-13 Released: 2014-05-14
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: 2.00 Å
R-Value Free: 0.223
R-Value Work: 0.173
R-Value Observed: 0.175

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg,d-mannonate and 2-keto-3-deoxy-d-gluconate

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

To be published.

Macromolecule Content

Total Structure Weight: 365.67 kDa
Atom Count: 26,541
Modelled Residue Count: 3,086
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CS2 Query on CS2 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain T [auth E] SDF format, chain V [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F]	I [auth A], L [auth B], T [auth E], V [auth F]	D-MANNONIC ACID C₆ H₁₂ O₇ RGHNJXZEOKUKBD-MBMOQRBOSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain T [auth E] Focus chain V [auth F]
KDG Query on KDG Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain N [auth C] SDF format, chain Y [auth G] SDF format, chain Q [auth D] MOL2 format, chain BA [auth H] MOL2 format, chain N [auth C] MOL2 format, chain Y [auth G] MOL2 format, chain Q [auth D] mmCIF format, chain BA [auth H] mmCIF format, chain N [auth C] mmCIF format, chain Y [auth G] mmCIF format, chain Q [auth D]	BA [auth H], N [auth C], Q [auth D], Y [auth G]	2-KETO-3-DEOXYGLUCONATE C₆ H₁₀ O₆ WPAMZTWLKIDIOP-WVZVXSGGSA-N		Interactions Focus chain BA [auth H] Focus chain N [auth C] Focus chain Q [auth D] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain N [auth C] Focus chain Q [auth D] Focus chain Y [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Z [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain Z [auth G]	Z [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Z [auth G] Interactions & Density Focus chain Z [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain W [auth F] MOL2 format, chain J [auth A] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain W [auth F] mmCIF format, chain J [auth A] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain W [auth F]	J [auth A], O [auth C], R [auth D], W [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain O [auth C] Focus chain R [auth D] Focus chain W [auth F] Interactions & Density Focus chain J [auth A] Focus chain O [auth C] Focus chain R [auth D] Focus chain W [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth H] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F]	AA [auth G] CA [auth H] K [auth A] M [auth B] P [auth C] AA [auth G], CA [auth H], K [auth A], M [auth B], P [auth C], S [auth D], U [auth E], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.223
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.242	α = 90
b = 167.263	β = 90
c = 168.863	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-14
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description