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- PDB-3ifz: crystal structure of the first part of the Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 3ifz
Titlecrystal structure of the first part of the Mycobacterium tuberculosis DNA gyrase reaction core: the breakage and reunion domain at 2.7 A resolution
ComponentsDNA gyrase subunit A
KeywordsISOMERASE / DNA gyrase / GyrA / Breakage and reunion domain / Type II topoisomerase / tuberculosis / quinolone binding site / DNA binding site / Antibiotic resistance / ATP-binding / DNA-binding / Nucleotide-binding / Topoisomerase
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily / EF-hand calcium-binding domain.
Similarity search - Domain/homology
DNA gyrase subunit A / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 ...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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,2336
Polymers113,9512
Non-polymers2824
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-57 kcal/mol
Surface area43740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.915, 109.660, 101.996
Angle α, β, γ (deg.)90.00, 120.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA gyrase subunit A


Mass: 56975.371 Da / Num. of mol.: 2 / Fragment: Breakage and reunion domain (N-terminal domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: gyrA, MT0006, MTCY10H4.04, Rv0006 / Plasmid: pET-29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2
References: UniProt: Q07702, UniProt: P9WG47*PLUS, EC: 5.99.1.3
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, MPD, PEG 4000, pH 7.5, 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: May 15, 2009
Details: Kirkpatrick-Baez pair of bi-morph 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: 2.7→35 Å / Num. all: 42989 / Num. obs: 42396 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.44 % / Biso Wilson estimate: 63.435 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.087 / Net I/σ(I): 12.46
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.17 / Num. unique all: 3186 / Rsym value: 0.75 / % possible all: 98

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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: 1AB4

1ab4


Resolution: 2.7→19.9 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 2125 5.01 %RANDOM
Rwork0.1921 ---
all0.1941 42989 --
obs0.1941 42396 99.19 %-
Displacement parametersBiso mean: 57.48 Å2
Baniso -1Baniso -2Baniso -3
1-7.55131075 Å20 Å2-3.59159366 Å2
2--2.35491207 Å20 Å2
3----9.90622282 Å2
Refine analyzeLuzzati coordinate error obs: 0.3428 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7534 0 18 222 7774
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00476632
X-RAY DIFFRACTIONt_angle_deg0.719103382
X-RAY DIFFRACTIONt_dihedral_angle_d22.4416030
X-RAY DIFFRACTIONt_trig_c_planes0.0042172
X-RAY DIFFRACTIONt_gen_planes0.00811235
X-RAY DIFFRACTIONt_it1.012766320
X-RAY DIFFRACTIONt_nbd0.031475
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3155 145 4.65 %
Rwork0.2443 2970 -
all0.2475 3115 -
obs-3123 99.19 %

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