1TVL | pdb_00001tvl

Structure of YTNJ from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1TVL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-06-29 Released: 2004-07-13
Deposition Author(s): Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.228 (Depositor), 0.271 (DCC)
R-Value Work:
0.207 (Depositor)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1TVL

This is version 1.4 of the entry. See complete history.

Literature

Structure of YTNJ from Bacillus subtilis

Gorman, J., Shapiro, L.

To be published.

Macromolecule Content

Total Structure Weight: 50.83 kDa
Atom Count: 3,299
Modeled Residue Count: 390
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein YTNJ	A	454	Bacillus subtilis	Mutation(s): 0 Gene Names: YTNJ EC: 1.14.13 (PDB Primary Data), 1.14.14 (UniProt)
UniProt
Find proteins for O34974 (Bacillus subtilis (strain 168)) Explore O34974 Go to UniProtKB: O34974
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34974
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.228 (Depositor), 0.271 (DCC)
R-Value Work: 0.207 (Depositor)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.941	α = 90
b = 85.941	β = 90
c = 196.298	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-07-13

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-07-13
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references

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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.