3E57 | pdb_00003e57

Crystal structure of Tm1382, a putative Nudix hydrolase

PDB DOI: https://doi.org/10.2210/pdb3E57/pdb

Classification: structural genomics, unknown function
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-13 Released: 2008-09-30
Deposition Author(s): Choi, W., Cooper, D.R., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.240 (Depositor), 0.252 (DCC)
R-Value Work:
0.199 (Depositor), 0.205 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3E57

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

Literature

Crystal structure of Tm1382, a putative Nudix hydrolase

Choi, W., Cooper, D.R., Derewenda, Z.S.

To be published.

Macromolecule Content

Total Structure Weight: 49.14 kDa
Atom Count: 3,192
Modeled Residue Count: 363
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein Tm1382	A, B	211	Thermotoga maritima	Mutation(s): 0 Gene Names: TM_1382
UniProt
Find proteins for Q9X1A2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1A2 Go to UniProtKB: Q9X1A2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X1A2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.240 (Depositor), 0.252 (DCC)
R-Value Work: 0.199 (Depositor), 0.205 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.589	α = 90
b = 62.879	β = 98.37
c = 73.896	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

Derewenda, Z.S.

Integrated Center for Structure and Function Innovation (ISFI)

Revision History (Full details and data files)

Version 1.0: 2008-09-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.