4KT2 | pdb_00004kt2

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

PDB DOI: https://doi.org/10.2210/pdb4KT2/pdb

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

Deposited: 2013-05-19 Released: 2014-05-21
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:
0.182 (Depositor), 0.179 (DCC)
R-Value Work:
0.149 (Depositor), 0.147 (DCC)
R-Value Observed:
0.151 (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: 366.26 kDa
Atom Count: 26,989
Modeled Residue Count: 3,100
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): 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 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
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain QA [auth H] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain HA [auth F] SDF format, chain CA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain QA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain PA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain QA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] HA [auth F] IA [auth F] L [auth A] LA [auth G] CA [auth E], HA [auth F], IA [auth F], L [auth A], LA [auth G], M [auth A], MA [auth G], PA [auth H], Q [auth B], QA [auth H], U [auth C], V [auth C], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain OA [auth H] SDF format, chain KA [auth G] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain OA [auth H] MOL2 format, chain KA [auth G] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D] mmCIF format, chain OA [auth H] mmCIF format, chain KA [auth G]	BA [auth E] FA [auth F] GA [auth F] K [auth A] KA [auth G] BA [auth E], FA [auth F], GA [auth F], K [auth A], KA [auth G], OA [auth H], P [auth B], T [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain K [auth A] Focus chain KA [auth G] Focus chain OA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain K [auth A] Focus chain KA [auth G] Focus chain OA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain I [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain I [auth A]	DA [auth F], I [auth A], N [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain DA [auth F] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain JA [auth G] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain NA [auth H] SDF format, chain J [auth A] SDF format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain NA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain NA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth E]	AA [auth E] EA [auth F] J [auth A] JA [auth G] NA [auth H] AA [auth E], EA [auth F], J [auth A], JA [auth G], NA [auth H], O [auth B], S [auth C], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain J [auth A] Focus chain JA [auth G] Focus chain NA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain J [auth A] Focus chain JA [auth G] Focus chain NA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.182 (Depositor), 0.179 (DCC)
R-Value Work: 0.149 (Depositor), 0.147 (DCC)
R-Value Observed: 0.151 (Depositor)

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-05-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-21
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description