4MB6 | pdb_00004mb6

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis.

PDB DOI: https://doi.org/10.2210/pdb4MB6/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pseudotuberculosis IP 32953
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-19 Released: 2013-09-04
Deposition Author(s): Pavithra, G.C., Kim, J., Hegde, R.P., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.238 (Depositor), 0.244 (DCC)
R-Value Work:
0.184 (Depositor), 0.191 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis

Pavithra, G.C., Kim, J., Hegde, R.P., Almo, S.C., Ramagopal, U.A.

To be published.

Macromolecule Content

Total Structure Weight: 20.19 kDa
Atom Count: 1,429
Modeled Residue Count: 183
Deposited Residue Count: 187
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A	187	Yersinia pseudotuberculosis IP 32953	Mutation(s): 0 Gene Names: apt, YPTB0991 EC: 2.4.2.7
UniProt
Find proteins for Q66DQ2 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66DQ2 Go to UniProtKB: Q66DQ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q66DQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.238 (Depositor), 0.244 (DCC)
R-Value Work: 0.184 (Depositor), 0.191 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.56	α = 90
b = 78.38	β = 112.98
c = 54.01	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Ramagopal, U.A.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 1.1: 2023-09-20
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.