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- PDB-2xcq: The 2.98A crystal structure of the catalytic core (B'A' region) o... -

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Basic information

Entry
Database: PDB / ID: 2xcq
TitleThe 2.98A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus DNA Gyrase
ComponentsDNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
KeywordsISOMERASE
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 / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : ...Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / 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 / DNA gyrase subunit B, TOPRIM domain / Topoisomerase (Topo) IIA-type catalytic domain profile. / 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, 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, 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 / Gyrase A; domain 2 / 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 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsBax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. ...Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / Lewis, C.J. / May, E.W. / Singh, O. / Spitzfaden, C. / Shen, C. / Shillings, A. / Theobald, A.F. / Wohlkonig, A. / Pearson, N.D. / Gwynn, M.N.
CitationJournal: Nature / Year: 2010
Title: Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.
Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / ...Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / Lewis, C.J. / May, E.W. / Saunders, M.R. / Singh, O. / Spitzfaden, C. / Shen, C. / Shillings, A. / Theobald, A.F. / Wohlkonig, A. / Pearson, N.D. / Gwynn, M.N.
History
DepositionApr 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)82,3451
Polymers82,3451
Non-polymers00
Water181
1
A: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A

A: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)164,6902
Polymers164,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_575x,x-y+2,-z+1/61
Buried area7970 Å2
ΔGint-9.2 kcal/mol
Surface area58970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.118, 90.118, 416.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A


Mass: 82344.898 Da / Num. of mol.: 1
Fragment: C-TERMINAL 27KDA DOMAIN, RESIDUES 410-644, N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491
Source method: isolated from a genetically manipulated source
Details: C-TERMINUS GYRB (A644) FUSED TO N-TERMINUS GYRA (A1002)
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P66937, UniProt: Q99XG5, EC: 5.99.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.38 Å3/Da / Density % sol: 63.33 % / Description: NONE
Crystal growDetails: 12.75% PEG 3350, 85MM MGFORMATE, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93926
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93926 Å / Relative weight: 1
ReflectionResolution: 2.98→14 Å / Num. obs: 19434 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 99 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 2.98→3.14 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCO

2xco


Resolution: 2.98→13.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.879 / SU B: 21.572 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28637 1076 5.2 %RANDOM
Rwork0.20506 ---
obs0.20914 19434 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.425 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.98→13.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 0 1 5153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9767033
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023907
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.22487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3850.83234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55355206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.71461988
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.33481827
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.98→3.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 85 -
Rwork0.366 1391 -
obs--99.9 %
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)
18.4005-0.18840.98276.5603-0.84967.97270.16650.42891.331-0.3512-0.0613-0.6171-1.96750.9417-0.10511.0235-0.38510.02620.94190.33180.6502-1.6399107.18097.7823
22.1721-0.2290.06522.27731.12713.23690.18290.18470.3533-0.2931-0.23530.3146-0.8392-0.03720.05240.5569-0.1891-0.12510.42390.27190.4385-31.3577112.841941.939
35.81371.24481.42896.66181.42213.26480.1985-0.23480.69860.68550.0922-0.7964-0.96381.4181-0.29071.0251-0.6654-0.05710.85860.11540.6279-6.8608125.739761.1345
42.89080.7949-0.372210.4503-0.03772.58210.1297-0.187-0.20690.161-0.49150.41140.31-1.39320.36190.2144-0.2271-0.17041.2060.0750.7252-61.662983.587532.8751
533.964813.67655.809810.2082-6.48632.50290.04232.1026-1.8444-1.37930.9851.21321.819-2.1991-1.02731.11360.0384-0.3331.07450.1411.1113-28.559298.63145.3973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A411 - 543
2X-RAY DIFFRACTION1A581 - 610
3X-RAY DIFFRACTION1A2001
4X-RAY DIFFRACTION2A1027 - 1244
5X-RAY DIFFRACTION2A1329 - 1368
6X-RAY DIFFRACTION2A1461 - 1491
7X-RAY DIFFRACTION3A1245 - 1328
8X-RAY DIFFRACTION4A1369 - 1460
9X-RAY DIFFRACTION5A544 - 580

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