2RK9 | pdb_00002rk9

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01

PDB DOI: https://doi.org/10.2210/pdb2RK9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio splendidus 12B01
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-10-16 Released: 2007-10-30
Deposition Author(s): Tyagi, R., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.229 (Depositor), 0.231 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2RK9

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

Literature

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01.

Tyagi, R., Eswaramoorthy, S., Sauder, J.M., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 33.71 kDa
Atom Count: 2,123
Modeled Residue Count: 233
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B	145	Vibrio splendidus 12B01	Mutation(s): 1 Gene Names: 84385607, V12B01_25774
UniProt
Find proteins for A0A1C3J8J6 (Vibrio celticus) Explore A0A1C3J8J6 Go to UniProtKB: A0A1C3J8J6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1C3J8J6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.229 (Depositor), 0.231 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.704	α = 90
b = 76.954	β = 92
c = 42.395	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-10-30

Deposition Author(s):

Eswaramoorthy, S.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-10-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2018-11-14
Changes: Data collection, Structure summary
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2021-10-20
Changes: Database references
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary

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.