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- PDB-2xco: The 3.1A crystal structure of the catalytic core (B'A' region) of... -

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Basic information

Entry
Database: PDB / ID: 2xco
TitleThe 3.1A 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) complex / 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 ...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 / 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 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 / 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 / OTHER / Resolution: 3.1 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 B, DNA GYRASE SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3852
Polymers82,3451
Non-polymers401
Water181
1
A: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
hetero molecules

A: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,7704
Polymers164,6902
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_575x,x-y+2,-z+1/61
Buried area3910 Å2
ΔGint-15.2 kcal/mol
Surface area40600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.917, 89.917, 410.583
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1500-

CA

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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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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: 3.46 Å3/Da / Density % sol: 64.19 % / Description: NONE
Crystal growpH: 8
Details: 6% PEG 1,000, 0.15M CALCIUM ACETATE, 100MM IMIDAZOLE, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. obs: 17229 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.1→24.732 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 880 5.1 %
Rwork0.2169 --
obs0.2204 17229 91.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.568 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 61.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.883 Å2-0 Å2-0 Å2
2--3.883 Å2-0 Å2
3----7.7659 Å2
Refinement stepCycle: LAST / Resolution: 3.1→24.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 1 1 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045005
X-RAY DIFFRACTIONf_angle_d0.8066754
X-RAY DIFFRACTIONf_dihedral_angle_d19.1851887
X-RAY DIFFRACTIONf_chiral_restr0.055773
X-RAY DIFFRACTIONf_plane_restr0.003889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.29390.33281540.27132730X-RAY DIFFRACTION95
3.2939-3.54760.34281400.23792724X-RAY DIFFRACTION94
3.5476-3.90330.28041600.21382736X-RAY DIFFRACTION93
3.9033-4.46530.25111580.1782702X-RAY DIFFRACTION92
4.4653-5.61490.23451460.18832699X-RAY DIFFRACTION89
5.6149-24.73270.31371220.23592758X-RAY DIFFRACTION85
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)
10.4711-0.1890.18080.2916-0.24760.2179-0.04480.01630.3550.0801-0.0739-0.0816-0.57560.2485-0.00040.3613-0.07270.02130.35260.0910.3115-3.1142105.44547.4663
20.02820.0146-0.00260.03440.03350.021-0.08290.2013-0.1722-0.1804-0.08620.7045-0.1374-0.2068-0.00070.3861-0.0842-0.13450.79240.21370.4724-28.123999.20416.2874
30.7188-0.2601-0.23320.62110.14420.75640.06970.1049-0.0019-0.0468-0.04990.0766-0.0861-0.026-00.2093-0.06680.00260.17410.01760.1895-31.7582112.366241.4734
4-0.0055-0.0736-0.03880.16180.07880.0363-0.01980.02630.24220.11580.04290.0252-0.26880.38320.0990.1687-0.4263-0.0163-0.0823-0.08040.2163-7.0573124.896760.3905
50.1661-0.1447-0.14390.02730.00980.10480.0357-0.07870.07070.0571-0.18070.1450.0076-0.3717-0.02220.076-0.1267-0.0230.5531-0.05040.2551-61.98983.198432.4391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((CHAIN A AND (RESID 413:543 OR RESID 581:606)))
2X-RAY DIFFRACTION2((CHAIN A AND (RESID 544:580)))
3X-RAY DIFFRACTION3((CHAIN A AND (RESID 1027:1244 OR RESID 1329:1368 OR RESID 1461:1490)))
4X-RAY DIFFRACTION4((CHAIN A AND (RESID 1245:1328)))
5X-RAY DIFFRACTION5((CHAIN A AND (RESID 1369:1460)))

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