2RGY | pdb_00002rgy

Crystal structure of transcriptional regulator of LacI family from Burkhoderia phymatum

PDB DOI: https://doi.org/10.2210/pdb2RGY/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Paraburkholderia phymatum STM815
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-05 Released: 2007-10-23
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.267 (Depositor), 0.269 (DCC)
R-Value Work:
0.210 (Depositor), 0.226 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2RGY

This is version 1.3 of the entry. See complete history.

Literature

Structural analysis of transcription regulator of LacI family from Burkholderia phymatum.

Agarwal, R., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 32.17 kDa
Atom Count: 2,296
Modeled Residue Count: 275
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A	290	Paraburkholderia phymatum STM815	Mutation(s): 0 Gene Names: BphyDRAFT_4885 EC: 5.1.1.1
UniProt
Find proteins for B2JNW3 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JNW3 Go to UniProtKB: B2JNW3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2JNW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.267 (Depositor), 0.269 (DCC)
R-Value Work: 0.210 (Depositor), 0.226 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.543	α = 90
b = 118.777	β = 90
c = 85.439	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-10-30
Changes: Data collection, Database references, 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.