3VCN

Crystal structure of mannonate dehydratase (target EFI-502209) from Caulobacter crescentus CB15

PDB DOI: https://doi.org/10.2210/pdb3VCN/pdb

Classification: LYASE
Organism(s): Caulobacter vibrioides
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-04 Released: 2012-01-25
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: 1.45 Å
R-Value Free: 0.188
R-Value Work: 0.130
R-Value Observed: 0.132

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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: 95.24 kDa
Atom Count: 7,273
Modelled Residue Count: 806
Deposited Residue Count: 850
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNONATE DEHYDRATASE	A, B [auth C]	425	Caulobacter vibrioides	Mutation(s): 0 Gene Names: CC_0532, PRK15072 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 4 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 H [auth A] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth C]	D [auth A], H [auth A], I [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth C]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C]	E [auth A], K [auth C]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C]	F [auth A], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain M [auth C] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth C] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth C]	C [auth A], G [auth A], J [auth C], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth C] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.188
R-Value Work: 0.130
R-Value Observed: 0.132
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.302	α = 90
b = 116.302	β = 90
c = 118.078	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2012-03-07
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description