2Q01

Crystal structure of glucuronate isomerase from Caulobacter crescentus

PDB DOI: https://doi.org/10.2210/pdb2Q01/pdb

Classification: ISOMERASE
Organism(s): Caulobacter vibrioides CB15
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-05-18 Released: 2007-05-29
Deposition Author(s): Patskovsky, Y., Bonanno, J., Sridhar, V., Sauder, J.M., Freeman, J., Powell, A., Koss, J., Groshong, C., Gheyi, T., Wasserman, S.R., Raushel, F., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Glucuronate Isomerase from Caulobacter crescentus.

Patskovsky, Y., Bonanno, J., Sridhar, V., Sauder, J.M., Freeman, J., Powell, A., Koss, J., Groshong, C., Gheyi, T., Wasserman, S.R., Raushel, F., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 169.14 kDa
Atom Count: 12,130
Modelled Residue Count: 1,439
Deposited Residue Count: 1,491
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uronate isomerase	A, B, C	497	Caulobacter vibrioides CB15	Mutation(s): 0 Gene Names: uxaC, CC_1490 EC: 5.3.1.12
UniProt
Find proteins for Q9A874 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9A874 Go to UniProtKB: Q9A874
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9A874
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.251 (Depositor), 0.250 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.332	α = 90
b = 190.176	β = 90
c = 319.29	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Refinement description