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- PDB-2zjt: Crystal structure of dna gyrase B' domain sheds lights on the mec... -

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Basic information

Entry
Database: PDB / ID: 2zjt
TitleCrystal structure of dna gyrase B' domain sheds lights on the mechanism for T-segment navigation
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / DNA gyrase / GyrB-CTD / Toprim / Tail / DNA topoisomerase II / G-segment / T-segment / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / DNA binding ...DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / DNA binding / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Dna Ligase; domain 1 - #440 / Rossmann fold - #670 / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA ...Dna Ligase; domain 1 - #440 / Rossmann fold - #670 / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Dna Ligase; domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsFu, G.S. / Zhu, D.Y. / Hu, Y.L. / Wang, D.C.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation
Authors: Fu, G.S. / Wu, J.J. / Liu, W. / Zhu, D.Y. / Hu, Y.L. / Deng, J. / Zhang, X.E. / Bi, L.J. / Wang, D.C.
History
DepositionMar 10, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,8742
Polymers55,8742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-16.3 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.831, 52.763, 192.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA gyrase subunit B


Mass: 27937.010 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gyrB / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS, B834(DE3)
References: UniProt: P0C5C5, UniProt: P9WG45*PLUS, EC: 5.99.1.3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.401895 Å3/Da / Density % sol: 48.79044 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% PEG 3350, 50mM sodium acetate, 0.2M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.97947, 1.0000
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 6, 2006
RIGAKU RAXIS IV++2IMAGE PLATEOct 26, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979471
211
31.54181
ReflectionResolution: 2.8→36.7 Å / Num. all: 13938 / Num. obs: 13423 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 80.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 9.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1979 / Rsym value: 0.348 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.03 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1177400.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 654 5.1 %RANDOM
Rwork0.244 ---
obs0.244 12741 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2337 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 58.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---1.91 Å20 Å2
3---2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 0 0 2962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 96 5.3 %
Rwork0.341 1731 -
obs--81 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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