3N2L

2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961

PDB DOI: https://doi.org/10.2210/pdb3N2L/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-18 Released: 2010-06-02
Deposition Author(s): Halavaty, A.S., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.269
R-Value Work: 0.222
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961

Halavaty, A.S., Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 210.54 kDa
Atom Count: 12,436
Modelled Residue Count: 1,488
Deposited Residue Count: 1,904
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotate phosphoribosyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	238	Vibrio cholerae	Mutation(s): 0 Gene Names: pyrE, VC_0211 EC: 2.4.2.10
UniProt
Find proteins for Q9KVD5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVD5 Go to UniProtKB: Q9KVD5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KVD5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth H] SDF format, chain K [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H]	I [auth A], J [auth H], K [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth H] Focus chain K [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth H] Focus chain K [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.269
R-Value Work: 0.222
R-Value Observed: 0.224
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33N2L

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.587	α = 90
b = 76.712	β = 92.63
c = 133.944	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3N2L

2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961

2.1 Angstrom resolution crystal structure of an Orotate Phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)