3PK7

Crystal structure of D-mannonate dehydratase from Chromohalobacter salexigens with MG and Glycerol bound in the active site

PDB DOI: https://doi.org/10.2210/pdb3PK7/pdb

Classification: ISOMERASE
Organism(s): Chromohalobacter salexigens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-11 Released: 2011-11-16
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: 0.184
R-Value Work: 0.158
R-Value Observed: 0.159

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 with MG and Glycerol bound in the active site

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

To be published.

Macromolecule Content

Total Structure Weight: 364.7 kDa
Atom Count: 27,832
Modelled Residue Count: 3,126
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
Mandelate racemase/muconate lactonizing enzyme	A, B, C, D, E A, B, C, D, E, F, G, H	405	Chromohalobacter salexigens	Mutation(s): 0 Gene Names: Csal_2974
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] S [auth E] J [auth A], L [auth B], N [auth C], P [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth D] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.184
R-Value Work: 0.158
R-Value Observed: 0.159
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
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-16
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3PK7

Crystal structure of D-mannonate dehydratase from Chromohalobacter salexigens with MG and Glycerol bound in the active site

Crystal structure of D-mannonate dehydratase from Chromohalobacter salexigens with MG and Glycerol bound in the active site

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)