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- PDB-3m4i: Crystal structure of the second part of the Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 3m4i
TitleCrystal structure of the second part of the Mycobacterium tuberculosis DNA gyrase reaction core: the TOPRIM domain at 1.95 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPiton, J. / Petrella, S. / Aubry, A. / 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
DepositionMar 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5372
Polymers27,4191
Non-polymers1181
Water2,648147
1
A: DNA gyrase subunit B
hetero molecules

A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0754
Polymers54,8392
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2330 Å2
ΔGint-15 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.815, 52.815, 190.462
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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 49.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: AMMONIUM SULFATE, TRIS, PEG 4000, CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2010
Details: KIRKPATRICK-BAEZ PAIR OF BIMORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→29.39 Å / Num. all: 20688 / Num. obs: 20626 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2913 / Rsym value: 0.629 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AB4

1ab4


Resolution: 1.95→17 Å / Cor.coef. Fo:Fc: 0.9372 / Cor.coef. Fo:Fc free: 0.9277 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1009 4.92 %RANDOM
Rwork0.2099 ---
obs0.2109 20517 99.69 %-
all-20517 --
Displacement parametersBiso mean: 39.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.8508 Å20 Å20 Å2
2--0.8508 Å20 Å2
3----1.7015 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: LAST / Resolution: 1.95→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 8 147 1637
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071513HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972043HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d536SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes41HARMONIC2
X-RAY DIFFRACTIONt_gen_planes215HARMONIC5
X-RAY DIFFRACTIONt_it1513HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion15.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion197SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1779SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.06 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.266 150 5.21 %
Rwork0.2084 2727 -
all0.2113 2877 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8775-0.0822-0.51281.70480.88823.3292-0.01040.4122-0.18070.02830.050.02640.2399-0.0404-0.0396-0.1425-0.0120.00840.0812-0.0414-0.0689-7.2823-7.9956-14.8011
27.68791.9308-1.98731.9659-0.49691.89120.09920.14850.35350.1036-0.08560.04060.0503-0.0557-0.0136-0.0947-0.01720.00960.06580.041-0.072917.02648.2075-12.7187
33.3461.85472.36850.3469-0.47646.62030.0160.18430.09480.02270.09050.00110.00190.2438-0.1065-0.11330.00040.0441-0.0152-0.0109-0.0657-2.306-1.4238-5.2022

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