3SCZ | pdb_00003scz

Combining crystallographic, thermodynamic, and molecular dynamics studies of Mycobacterium tuberculosis purine nucleoside phosphorylase

PDB DOI: https://doi.org/10.2210/pdb3SCZ/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-06-08 Released: 2012-06-20
Deposition Author(s): de Azevedo Jr., W.F., Caceres, R.A., Timmers, L.F.S.M., Ducati, R.G., Rosado, L.A., Basso, L.A., Santos, D.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Combining crystallographic, thermodynamic, and molecular dynamics studies of Mycobacterium tuberculosis purine nucleoside phosphorylase

de Azevedo Jr., W.F.

To be published.

Macromolecule Content

Total Structure Weight: 55.47 kDa
Atom Count: 4,101
Modeled Residue Count: 525
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B	268	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: punA, deoD, Rv3307, MT3406, MTV016.06 EC: 2.4.2.1
UniProt
Find proteins for P9WP01 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP01 Go to UniProtKB: P9WP01
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WP01
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HPA Query on HPA Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	HYPOXANTHINE C₅ H₄ N₄ O FDGQSTZJBFJUBT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.174 (Depositor), 0.180 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.59	α = 90
b = 115.59	β = 90
c = 86.3	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-06-20

Deposition Author(s):

de Azevedo Jr., W.F.

Timmers, L.F.S.M.

Revision History (Full details and data files)

Version 1.0: 2012-06-20
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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.