2A1V | pdb_00002a1v

Crystal structure of Deinococcus radiodurans protein DR2400, Pfam domain DUF419

PDB DOI: https://doi.org/10.2210/pdb2A1V/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Deinococcus radiodurans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-06-21 Released: 2005-07-26
Deposition Author(s): Ramagopal, U.A., Patskovsky, Y.V., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.225 (Depositor), 0.232 (DCC)
R-Value Work:
0.161 (Depositor), 0.173 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2A1V

This is version 1.5 of the entry. See complete history.

Literature

Hypothetical protein from Deinococcus radiodurans

Ramagopal, U.A., Patskovsky, Y.V., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 16.3 kDa
Atom Count: 1,264
Modeled Residue Count: 138
Deposited Residue Count: 144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein	A	144	Deinococcus radiodurans	Mutation(s): 0
UniProt
Find proteins for Q9RRT5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RRT5 Go to UniProtKB: Q9RRT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RRT5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.225 (Depositor), 0.232 (DCC)
R-Value Work: 0.161 (Depositor), 0.173 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.549	α = 90
b = 82.549	β = 90
c = 35.991	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
SHELXD	phasing
SHELXE	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-07-26

Deposition Author(s):

Ramagopal, U.A.

Patskovsky, Y.V.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2005-07-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-02-03
Changes: Database references, Structure summary
Version 1.5: 2024-02-14
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.