3CWV | pdb_00003cwv

Crystal structure of B-subunit of the DNA gyrase from Myxococcus xanthus

PDB DOI: https://doi.org/10.2210/pdb3CWV/pdb

Classification: ISOMERASE
Organism(s): Myxococcus xanthus DK 1622
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-04-22 Released: 2008-05-06
Deposition Author(s): Ramagopal, U.A., Toro, R., Meyer, A.J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.247 (Depositor), 0.244 (DCC)
R-Value Work:
0.209 (Depositor), 0.207 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of B-subunit of the DNA gyrase from Myxococcus xanthus.

Ramagopal, U.A., Toro, R., Meyer, A.J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 81.07 kDa
Atom Count: 5,479
Modeled Residue Count: 660
Deposited Residue Count: 738
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase, B subunit, truncated	A, B	369	Myxococcus xanthus DK 1622	Mutation(s): 0 Gene Names: MXAN_5971 EC: 5.6.2.2
UniProt
Find proteins for Q1CZR7 (Myxococcus xanthus (strain DK1622)) Explore Q1CZR7 Go to UniProtKB: Q1CZR7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1CZR7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.247 (Depositor), 0.244 (DCC)
R-Value Work: 0.209 (Depositor), 0.207 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.606	α = 90
b = 57.799	β = 127.23
c = 119.437	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL2Map	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-02-03
Changes: Database references, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references

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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.