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- PDB-3ig0: crystal structure of the second part of the Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 3ig0
Titlecrystal structure of the second part of the Mycobacterium tuberculosis DNA gyrase reaction core: the TOPRIM domain at 2.1 A resolution
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / DNA gyrase / GyrB / TOPRIM / Type II topoisomerase / tuberculosis / quinolone binding site / DNA binding site / ATP-binding / Nucleotide-binding / Topoisomerase
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 / Histidine kinase/HSP90-like ATPase / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B ...Dna Ligase; domain 1 - #440 / Rossmann fold - #670 / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / Histidine kinase/HSP90-like ATPase / 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 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPiton, J. / Aubry, A. / Delarue, M. / Mayer, C.
CitationJournal: Plos One / Year: 2010
Title: Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase.
Authors: Piton, J. / Petrella, S. / Delarue, M. / Andre-Leroux, G. / Jarlier, V. / Aubry, A. / Mayer, C.
History
DepositionJul 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: DNA gyrase subunit B


Theoretical massNumber of molelcules
Total (without water)27,4191
Polymers27,4191
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.870, 52.870, 190.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DNA gyrase subunit B


Mass: 27419.260 Da / Num. of mol.: 1 / Fragment: TOPRIM domain (C-terminal domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: HR37RV / Gene: gyrB, MT0005, MTCY10H4.03, Rv0005 / Plasmid: pRSF-2 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2
References: UniProt: P0C5C5, UniProt: P9WG45*PLUS, EC: 5.99.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, Tris, PEG 4000, Mgcl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2009 / Details: toroidal mirror + Si(111) monochromator
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→13.96 Å / Num. all: 16640 / Num. obs: 16487 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 33.746 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.141 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3347 / Rsym value: 0.556 / % possible all: 86.5

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Processing

Software
NameVersionClassification
Adxvdata processing
AMoREphasing
BUSTER-TNT2.5.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJT

2zjt


Resolution: 2.1→13.96 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 799 4.85 %RANDOM
Rwork0.2142 ---
all0.2159 16487 --
obs0.2159 16487 99.58 %-
Displacement parametersBiso mean: 40.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.76948031 Å20 Å20 Å2
2--0.76948031 Å20 Å2
3----1.53896062 Å2
Refine analyzeLuzzati coordinate error obs: 0.2861 Å
Refinement stepCycle: LAST / Resolution: 2.1→13.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 0 107 1581
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00415152
X-RAY DIFFRACTIONt_angle_deg0.83520322
X-RAY DIFFRACTIONt_dihedral_angle_d23.4753260
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005412
X-RAY DIFFRACTIONt_gen_planes0.0112145
X-RAY DIFFRACTIONt_it1.158151520
X-RAY DIFFRACTIONt_nbd0.037395
LS refinement shellResolution: 2.1→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3181 160 5.49 %
Rwork0.2354 2755 -
all0.2398 2915 -
obs-3212 99.58 %

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