3P93 | pdb_00003p93

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/pdb3P93/pdb

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

Deposited: 2010-10-15 Released: 2011-10-19
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:
0.241 (Depositor), 0.237 (DCC)
R-Value Work:
0.199 (Depositor), 0.196 (DCC)
R-Value Observed:
0.201 (Depositor)

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: 365.44 kDa
Atom Count: 26,363
Modeled Residue Count: 3,077
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
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 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CS2 Query on CS2 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain R [auth E] SDF format, chain T [auth F] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F]	J [auth A], L [auth B], R [auth E], T [auth F]	D-MANNONIC ACID C₆ H₁₂ O₇ RGHNJXZEOKUKBD-MBMOQRBOSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain R [auth E] Focus chain T [auth F]
KDG Query on KDG Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H]	N [auth C], P [auth D], V [auth G], X [auth H]	2-KETO-3-DEOXYGLUCONATE C₆ H₁₀ O₆ WPAMZTWLKIDIOP-WVZVXSGGSA-N		Interactions Focus chain N [auth C] Focus chain P [auth D] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain N [auth C] Focus chain P [auth D] Focus chain V [auth G] Focus chain X [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 E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [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 E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [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 E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [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 E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.241 (Depositor), 0.237 (DCC)
R-Value Work: 0.199 (Depositor), 0.196 (DCC)
R-Value Observed: 0.201 (Depositor)

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
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-19
Type: Initial release
Version 1.1: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description