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), 0.230 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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), 0.230 (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

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 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.