2P1Z | pdb_00002p1z

Crystal structure of phosphoribosyltransferase from Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb2P1Z/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium diphtheriae NCTC 13129
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-06 Released: 2007-04-03
Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.308 (Depositor), 0.310 (DCC)
R-Value Work:
0.226 (Depositor), 0.227 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of phosphoribosyltransferase from Corynebacterium diphtheriae

Chang, C., Li, H., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 38.6 kDa
Atom Count: 2,513
Modeled Residue Count: 326
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosyltransferase	A, B	180	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 3 Gene Names: pyrE, DIP2097 EC: 2.4.2.10
UniProt
Find proteins for Q8NM11 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NM11 Go to UniProtKB: Q8NM11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NM11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.308 (Depositor), 0.310 (DCC)
R-Value Work: 0.226 (Depositor), 0.227 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.438	α = 90
b = 103.709	β = 90
c = 39.417	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-04-03

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-04-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.