4F4R

Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop

PDB DOI: https://doi.org/10.2210/pdb4F4R/pdb

Classification: LYASE
Organism(s): Chromohalobacter israelensis DSM 3043
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-05-11 Released: 2012-06-27
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI), Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.171
R-Value Work: 0.145
R-Value Observed: 0.146

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 homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 48.2 kDa
Atom Count: 3,658
Modelled Residue Count: 408
Deposited Residue Count: 426
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	426	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.171
R-Value Work: 0.145
R-Value Observed: 0.146
Space Group: P 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.389	α = 90
b = 111.389	β = 90
c = 84.576	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Enzyme Function Initiative (EFI)

Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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4F4R

Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop

Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)