4GME

Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate

PDB DOI: https://doi.org/10.2210/pdb4GME/pdb

Classification: LYASE
Organism(s): Caulobacter vibrioides CB15
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-08-15 Released: 2012-09-12
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.196
R-Value Work: 0.156
R-Value Observed: 0.157

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Mannonate Dehydratase from Caulobacter Crescentus Cb15

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 95.41 kDa
Atom Count: 6,886
Modelled Residue Count: 806
Deposited Residue Count: 852
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 family	A, B [auth C]	426	Caulobacter vibrioides CB15	Mutation(s): 0 Gene Names: CC_0532 EC: 4.2.1.8
UniProt
Find proteins for Q9AAR4 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9AAR4 Go to UniProtKB: Q9AAR4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9AAR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CS2 Query on CS2 Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	D-MANNONIC ACID C₆ H₁₂ O₇ RGHNJXZEOKUKBD-MBMOQRBOSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth C]	D [auth A], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth C] MOL2 format, chain C [auth A] MOL2 format, chain G [auth C] mmCIF format, chain C [auth A] mmCIF format, chain G [auth C]	C [auth A], G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth C] Interactions & Density Focus chain C [auth A] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.196
R-Value Work: 0.156
R-Value Observed: 0.157
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.801	α = 90
b = 115.801	β = 90
c = 118.131	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-12

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-09-12
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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4GME

Crystal structure of mannonate dehydratase (target EFI-502209) from caulobacter crescentus cb15 complexed with magnesium and d-mannonate

Crystal Structure of Mannonate Dehydratase from Caulobacter Crescentus Cb15

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)