2RBB | pdb_00002rbb

Crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase family enzyme from Burkholderia phytofirmans PsJN

PDB DOI: https://doi.org/10.2210/pdb2RBB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paraburkholderia phytofirmans PsJN
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-09-18 Released: 2007-10-16
Deposition Author(s): Rao, K.N., 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: 1.82 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.239 (Depositor), 0.236 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase family enzyme from Burkholderia phytofirmans PsJN.

Rao, K.N., Sauder, J.M., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.66 kDa
Atom Count: 2,281
Modeled Residue Count: 256
Deposited Residue Count: 282
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	141	Paraburkholderia phytofirmans PsJN	Mutation(s): 2 Gene Names: BphytDRAFT_4892
UniProt
Find proteins for B2TEV0 (Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)) Explore B2TEV0 Go to UniProtKB: B2TEV0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2TEV0
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: 1.82 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.239 (Depositor), 0.236 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.23	α = 90
b = 83.23	β = 90
c = 99.59	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-16

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-10-16
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

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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.