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- PDB-3cwv: Crystal structure of B-subunit of the DNA gyrase from Myxococcus ... -

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Basic information

Entry
Database: PDB / ID: 3cwv
TitleCrystal structure of B-subunit of the DNA gyrase from Myxococcus xanthus
ComponentsDNA gyrase, B subunit, truncated
KeywordsISOMERASE / structural genomics / UNKNOWN FUNCTION / DNA Gyrase / B-Subunit / ATP-binding / Nucleotide-binding / Topoisomerase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA binding / ATP binding
Similarity search - Function
DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase (ATP-hydrolyzing)
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsRamagopal, U.A. / Toro, R. / Meyer, A.J. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of B-subunit of the DNA gyrase from Myxococcus xanthus.
Authors: Ramagopal, U.A. / Toro, R. / Meyer, A.J. / Burley, S.K. / Almo, S.C.
History
DepositionApr 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA gyrase, B subunit, truncated
B: DNA gyrase, B subunit, truncated


Theoretical massNumber of molelcules
Total (without water)81,0752
Polymers81,0752
Non-polymers00
Water6,215345
1
A: DNA gyrase, B subunit, truncated


Theoretical massNumber of molelcules
Total (without water)40,5371
Polymers40,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA gyrase, B subunit, truncated


Theoretical massNumber of molelcules
Total (without water)40,5371
Polymers40,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.606, 57.799, 119.437
Angle α, β, γ (deg.)90.000, 127.230, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein DNA gyrase, B subunit, truncated


Mass: 40537.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Strain: DK 1622 / Gene: MXAN_5971 / Plasmid: BC-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1CZR7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 15 % PEG 3350, 0.1 M Magnesium formate dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 2.5 % / Av σ(I) over netI: 11.7 / Number: 302348 / Rmerge(I) obs: 0.048 / Χ2: 0.8 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 120809 / % possible obs: 96.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.25097.310.0331.0752.5
3.334.299.810.0431.0452.5
2.913.3399.910.0491.0672.6
2.652.9199.810.0530.922.6
2.462.6599.810.0690.7292.6
2.312.4699.710.0920.6712.6
2.22.3199.710.1240.6322.5
2.12.298.710.160.592.5
2.022.192.710.2290.572.4
1.952.0277.510.2940.5442.2
ReflectionResolution: 1.95→50 Å / Num. obs: 62921 / % possible obs: 98 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.061 / Χ2: 0.799 / Net I/σ(I): 24
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.64 / Num. unique all: 5484 / Rsym value: 0.331 / Χ2: 0.544 / % possible all: 86.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.603 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3177 5 %RANDOM
Rwork0.209 ---
obs0.211 62920 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.882 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å2-1.74 Å2
2--1.78 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5105 0 0 345 5450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215257
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9537147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3365663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63821.867241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90715830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.761562
X-RAY DIFFRACTIONr_chiral_restr0.0890.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024071
X-RAY DIFFRACTIONr_nbd_refined0.2060.22371
X-RAY DIFFRACTIONr_nbtor_refined0.3130.33556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.4568
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.426
X-RAY DIFFRACTIONr_mcbond_it1.7481.53381
X-RAY DIFFRACTIONr_mcangle_it2.59325260
X-RAY DIFFRACTIONr_scbond_it3.93232131
X-RAY DIFFRACTIONr_scangle_it5.8064.51885
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 183 -
Rwork0.251 3647 -
all-3830 -
obs--81.25 %

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