3LXM | pdb_00003lxm

2.00 Angstrom resolution crystal structure of a catalytic subunit of an aspartate carbamoyltransferase (pyrB) from Yersinia pestis CO92

PDB DOI: https://doi.org/10.2210/pdb3LXM/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-25 Released: 2010-03-16
Deposition Author(s): Halavaty, A.S., Minasov, G., Dubrovska, I., Winsor, J., Shuvalova, L., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.217 (Depositor), 0.243 (DCC)
R-Value Work:
0.179 (Depositor), 0.209 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

2.00 Angstrom resolution crystal structure of a catalytic subunit of an aspartate carbamoyltransferase (pyrB) from Yersinia pestis CO92

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

To be published.

Macromolecule Content

Total Structure Weight: 112.22 kDa
Atom Count: 7,196
Modeled Residue Count: 849
Deposited Residue Count: 1,005
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase	A, B, C	335	Yersinia pestis CO92	Mutation(s): 0 Gene Names: pyrB, y0161, YPO3588, YP_3842 EC: 2.1.3.2
UniProt
Find proteins for Q8ZB39 (Yersinia pestis) Explore Q8ZB39 Go to UniProtKB: Q8ZB39
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZB39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217 (Depositor), 0.243 (DCC)
R-Value Work: 0.179 (Depositor), 0.209 (DCC)
R-Value Observed: 0.181 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.62	α = 90
b = 120.409	β = 90
c = 126.698	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-03-16
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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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.