3OW1

Crystal structure of D-mannonate dehydratase from Chromohalobacter salexigens complexed with MG

PDB DOI: https://doi.org/10.2210/pdb3OW1/pdb

Classification: LYASE
Organism(s): Chromohalobacter israelensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-17 Released: 2011-09-28
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: 1.80 Å
R-Value Free: 0.194
R-Value Work: 0.161
R-Value Observed: 0.163

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

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

To be published.

Macromolecule Content

Total Structure Weight: 366.39 kDa
Atom Count: 26,837
Modelled Residue Count: 3,092
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 israelensis	Mutation(s): 0 Gene Names: Csal_2974 EC: 4.2.1 (UniProt), 4.2.1.8 (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
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain IA [auth G] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain FA [auth F] SDF format, chain P [auth B] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain FA [auth F] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain PA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain FA [auth F] mmCIF format, chain P [auth B]	BA [auth E] EA [auth F] FA [auth F] IA [auth G] JA [auth G] BA [auth E], EA [auth F], FA [auth F], IA [auth G], JA [auth G], KA [auth G], L [auth A], M [auth A], OA [auth H], P [auth B], PA [auth H], T [auth C], U [auth C], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain HA [auth G] SDF format, chain J [auth A] SDF format, chain NA [auth H] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain K [auth A] SDF format, chain MA [auth H] SDF format, chain R [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain R [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain R [auth C]	AA [auth E] DA [auth F] HA [auth G] J [auth A] K [auth A] AA [auth E], DA [auth F], HA [auth G], J [auth A], K [auth A], MA [auth H], NA [auth H], O [auth B], R [auth C], S [auth C], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain HA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain HA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain I [auth A] SDF format, chain LA [auth H] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	CA [auth F] GA [auth G] I [auth A] LA [auth H] N [auth B] CA [auth F], GA [auth G], I [auth A], LA [auth H], N [auth B], Q [auth C], V [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain LA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain LA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.194
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.585	α = 90
b = 177.787	β = 102.62
c = 109.993	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-28
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description