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- PDB-4g3n: Mycobacterium tuberculosis gyrase type IIA topoisomerase C-termin... -

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Basic information

Entry
Database: PDB / ID: 4g3n
TitleMycobacterium tuberculosis gyrase type IIA topoisomerase C-terminal domain at 1.4 A resolution
ComponentsDNA gyrase subunit A
KeywordsISOMERASE / DNA gyrase C-terminal domain / beta-propeller / topoisomerase type IIA
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/topoisomerase IV, subunit A, C-terminal / 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 gyrase/topoisomerase IV, subunit A, C-terminal / 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 / 6 Propeller / Neuraminidase / EF-hand calcium-binding domain. / Mainly Beta
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: 1.4 Å
AuthorsDarmon, A. / Piton, J. / Petrella, S. / Aubry, A. / Mayer, C.
CitationJournal: Biochem.J. / Year: 2013
Title: Mycobacterium tuberculosis DNA gyrase possesses two functional GyrA-boxes.
Authors: Bouige, A. / Darmon, A. / Piton, J. / Roue, M. / Petrella, S. / Capton, E. / Forterre, P. / Aubry, A. / Mayer, C.
History
DepositionJul 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 13, 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 A


Theoretical massNumber of molelcules
Total (without water)35,3351
Polymers35,3351
Non-polymers00
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.700, 80.519, 88.182
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 A


Mass: 35334.746 Da / Num. of mol.: 1 / Fragment: UNP residues 512-838
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gyrA, MT0006, mtct10h4.04, MTCY10H4.04, Rv0006, rv006 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2
References: UniProt: Q07702, UniProt: P9WG47*PLUS, EC: 5.99.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES 100 mM PH 7.5, NaCl 200 mM, PEG 3350 20-30%, 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: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.4→44.09 Å / Num. obs: 53387 / % possible obs: 96.6 % / Biso Wilson estimate: 21.09 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZI0

1zi0


Resolution: 1.4→28 Å / Cor.coef. Fo:Fc: 0.9601 / Cor.coef. Fo:Fc free: 0.9473 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 2701 5.07 %RANDOM
Rwork0.1853 ---
obs0.1868 53241 96.58 %-
Displacement parametersBiso mean: 26.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.8801 Å20 Å20 Å2
2--1.1111 Å20 Å2
3----0.231 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: LAST / Resolution: 1.4→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 0 296 2607
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012365HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.093196HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d860SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes359HARMONIC5
X-RAY DIFFRACTIONt_it2365HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.22
X-RAY DIFFRACTIONt_other_torsion14.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion311SEMIHARMONIC5
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_contact3009SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2442 176 5.45 %
Rwork0.2366 3055 -
all0.237 3231 -
obs--96.58 %
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)
11.1447-0.143-0.22880.85630.29210.924-0.0325-0.11150.08620.06790.0061-0.01120.0730.10150.0264-0.0452-0.00360.0023-0.0093-0.0369-0.007926.09645.374819.3313
20.85140.17020.07060.8952-0.24330.8548-0.04530.09470.1924-0.036-0.0026-0.06940.03910.15330.0479-0.03540.0041-0.00880.0338-0.00090.006520.222944.59072.214
31.07030.3547-0.49591.2545-0.68661.6742-0.09030.06640.0855-0.14110.08770.08330.1944-0.01370.0026-0.0523-0.0031-0.0154-0.0533-0.0056-0.063610.498138.16951.014
41.1115-0.04550.56221.9291-1.57881.8544-0.0318-0.1331-0.0605-0.14260.07980.06230.2148-0.1885-0.048-0.03130.00980.0205-0.0459-0.0003-0.0389.353324.046515.7876
50.33020.2278-0.67270-1.22231.1188-0.00010.04130.0177-0.0280.0509-0.1219-0.006-0.0846-0.05080.0688-0.03110.0379-0.0451-0.02280.079923.448232.192519.1805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|512 - A|606 }A512 - 606
2X-RAY DIFFRACTION2{ A|607 - A|644 }A607 - 644
3X-RAY DIFFRACTION3{ A|645 - A|718 }A645 - 718
4X-RAY DIFFRACTION4{ A|719 - A|816 }A719 - 816
5X-RAY DIFFRACTION5{ A|817 - A|820 }A817 - 820

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