3N77 | pdb_00003n77

Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella typhimurium LT2

PDB DOI: https://doi.org/10.2210/pdb3N77/pdb

Classification: HYDROLASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-05-26 Released: 2010-08-18
Deposition Author(s): Frydrysiak, J., Cooper, D.R., Derewenda, U., Anderson, W.F., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI), Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.233 (Depositor), 0.245 (DCC)
R-Value Work:
0.167 (Depositor), 0.175 (DCC)
R-Value Observed:
0.170 (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

Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella typhimurium LT2

Frydrysiak, J., Cooper, D.R., Derewenda, U., Derewenda, Z.S.

To be published.

Macromolecule Content

Total Structure Weight: 32.83 kDa
Atom Count: 2,490
Modeled Residue Count: 282
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside triphosphatase nudI	A, B	144	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 4 Gene Names: nudI, STM2295, yfaO EC: 3.6.1 (PDB Primary Data), 3.6.1.12 (UniProt), 3.6.1.23 (UniProt), 3.6.1.9 (UniProt)
UniProt
Find proteins for Q8ZNF5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNF5 Go to UniProtKB: Q8ZNF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZNF5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.233 (Depositor), 0.245 (DCC)
R-Value Work: 0.167 (Depositor), 0.175 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.498	α = 90
b = 66.268	β = 113.87
c = 50.836	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-08-18

Deposition Author(s):

Derewenda, Z.S.

Integrated Center for Structure and Function Innovation (ISFI)

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-08-18
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, 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.