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- PDB-2xcr: The 3.5A crystal structure of the catalytic core (B'A' region) of... -

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Basic information

Entry
Database: PDB / ID: 2xcr
TitleThe 3.5A crystal structure of the catalytic core (B'A' region) of Staphylococcus aureus DNA Gyrase complexed with GSK299423 and DNA
Components
  • 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
  • 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
  • DNA 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 / DNA gyrase C-terminal domain, beta-propeller ...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
Chem-RXV / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
D: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
E: 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
F: 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
S: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
U: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
V: 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
W: 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,71110
Polymers353,7878
Non-polymers9232
Water0
1
B: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
D: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
E: 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
F: 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,3195
Polymers176,8584
Non-polymers4621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-68.8 kcal/mol
Surface area65870 Å2
MethodPISA
2
S: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
U: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
V: 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
W: 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,3915
Polymers176,9304
Non-polymers4621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-66.3 kcal/mol
Surface area64180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.260, 165.381, 308.431
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 B, DNA GYRASE SUBUNIT A /


Mass: 82328.898 Da / Num. of mol.: 4
Fragment: C-TERMINAL 27KDA DOMAIN, RESIDUES 410-644, N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C-TERMINUS GYRB (B644) FUSED TO N-TERMINUS GYRA (A2)
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P66937, UniProt: Q99XG5, EC: 5.99.1.3
#2: DNA chain 5'-D(*5UA*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'


Mass: 6099.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP *GP*CP*TP)-3'


Mass: 6135.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-RXV / 6-METHOXY-4-(2-{4-[([1,3]OXATHIOLO[5,4-C]PYRIDIN-6-YLMETHYL)AMINO]PIPERIDIN-1-YL}ETHYL)QUINOLINE-3-CARBONITRILE / GSK 299423


Mass: 461.579 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27N5O2S / Comment: antibiotic*YM
Compound detailsENGINEERED RESIDUE IN CHAIN B, TYR 123 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 123 TO PHE ...ENGINEERED RESIDUE IN CHAIN B, TYR 123 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 123 TO PHE ENGINEERED RESIDUE IN CHAIN S, TYR 123 TO PHE ENGINEERED RESIDUE IN CHAIN U, TYR 123 TO PHE
Nonpolymer detailsACETYLATED ADENOSINE : IN HIGHER RESOLUTION 2.1A STRUCTURE WAS EXTRA DENSITY ON ONE END OF DNA, ...ACETYLATED ADENOSINE : IN HIGHER RESOLUTION 2.1A STRUCTURE WAS EXTRA DENSITY ON ONE END OF DNA, MODELLED AS ACETYLATED ADENOSINE.
Sequence detailsTHIS IS A FUSION TRUNCATE IN WHICH THE C-TERMINAL RESIDUE OF GYRB (F644) IS FUSED TO THE N-TERMINAL ...THIS IS A FUSION TRUNCATE IN WHICH THE C-TERMINAL RESIDUE OF GYRB (F644) IS FUSED TO THE N-TERMINAL RESIDUE OF GYRA (A2). CATALYTIC TYROSINE (123) HAS BEEN MUTATED TO PHENYLALANINE

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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: 4.06 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1M NACL, 0.1M SOODIUM CITRATE PH 5.6, 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinOperator: NONE
ReflectionResolution: 3.5→24 Å / Num. obs: 62197 / % possible obs: 84.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 76.69 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 53.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→23.987 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2504 4.03 %
Rwork0.2082 --
obs0.2102 62197 84.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.467 Å2 / ksol: 0.246 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-68.3586 Å2-0 Å2-0 Å2
2---25.1122 Å2-0 Å2
3----44.0166 Å2
Refinement stepCycle: LAST / Resolution: 3.5→23.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22764 1599 66 0 24429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425033
X-RAY DIFFRACTIONf_angle_d0.90634103
X-RAY DIFFRACTIONf_dihedral_angle_d19.6579679
X-RAY DIFFRACTIONf_chiral_restr0.063821
X-RAY DIFFRACTIONf_plane_restr0.0044200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.56710.28930.28851989X-RAY DIFFRACTION49
3.5671-3.63970.34451640.29071993X-RAY DIFFRACTION53
3.6397-3.71850.31131670.28012262X-RAY DIFFRACTION61
3.7185-3.8047000.27132699X-RAY DIFFRACTION67
3.8047-3.89950.33211670.26182665X-RAY DIFFRACTION70
3.8995-4.00440.31631670.24432846X-RAY DIFFRACTION74
4.0044-4.1217000.23173201X-RAY DIFFRACTION79
4.1217-4.2540.27481670.23563525X-RAY DIFFRACTION91
4.254-4.40520.26371670.22163766X-RAY DIFFRACTION97
4.4052-4.58040.26061670.19883841X-RAY DIFFRACTION99
4.5804-4.78730.23311670.18273865X-RAY DIFFRACTION99
4.7873-5.03750.24331670.17483862X-RAY DIFFRACTION98
5.0375-5.34980.24581670.18093823X-RAY DIFFRACTION98
5.3498-5.75760.24231670.18773842X-RAY DIFFRACTION98
5.7576-6.32730.25331670.19473850X-RAY DIFFRACTION97
6.3273-7.2210.25971670.18183837X-RAY DIFFRACTION97
7.221-9.01660.19881670.15673863X-RAY DIFFRACTION96
9.0166-23.9880.18531660.15853964X-RAY DIFFRACTION95
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)
11.36270.15290.22681.357-0.16171.56480.1005-0.1812-0.2970.0151-0.06420.25120.53270.252801.2793-0.07050.02660.8060.08581.072525.8791-18.55657.0204
20.3962-0.052400.24790.48790.6860.02590.2218-0.11860.8131-0.08060.1275-0.07150.05710.02820.6953-0.04730.03070.99640.07280.540445.9596-0.492332.5952
30.02410.00810.22690.0680.06090.23530.1346-0.263-0.0727-0.0829-0.16290.6082-0.0624-0.3787-0.00891.3631-0.18670.18560.8490.04931.203717.48293.342735.0952
40.181-0.00980.07090.0255-0.0498-0.03660.3282-0.1318-0.03170.53880.02670.3493-0.2647-0.9269-0.00051.3130.08940.38121.63520.20542.107-23.74223.829515.4013
500.18320.43580.14980.0620.18330.5371-0.6447-0.19540.0182-0.25230.08650.2147-0.3458-0.00541.23180.10470.06810.91290.27530.863233.8675-16.725138.9438
61.4592-0.4601-0.09191.0055-0.6471.052-0.0133-0.22940.28340.328-0.1451-0.015-0.78320.30150.00020.8904-0.17860.11030.85-0.02820.957431.954528.15069.2264
70.60850.15850.31251.1258-0.10260.5178-0.23930.1721-0.0738-0.3358-0.0783-0.02970.13410.4259-0.41080.54780.1840.10710.891600.630844.2682-3.6542-16.9896
80.0673-0.14410.0140.0295-0.00680.16150.09470.09570.0599-0.34940.53260.85440.0319-0.4280.00051.06930.06790.08340.94510.14991.342816.64344.84-18.6254
90.2430.0388-0.06860.0384-0.11910.0672-0.1294-0.0664-0.7051-0.70370.72080.2638-0.5725-0.8419-0.00081.11460.19-0.00181.70520.32391.8327-20.281920.69413.0912
10-0.036-0.1-0.14270.39030.06870.13950.27110.17750.0972-0.667-0.6123-0.069-0.08540.4903-0.00641.0502-0.13070.1491.0110.05090.956139.387715.9826-23.4951
110.6838-0.2801-0.18940.7450.37671.5243-0.03570.1044-0.0486-0.09490.0412-0.0817-0.71930.6291-00.8232-0.17260.04951.159601.045449.1604-3.79284.4167
120.7803-0.27430.09790.1563-0.50840.5102-0.1788-0.20070.1391-0.4249-0.0421-0.0344-0.86530.09210.00041.4429-0.0433-0.11421.0512-0.06950.925329.989515.2991110.0784
130.1031-0.18660.2156-0.0012-0.0290.25340.2477-0.2315-0.7753-0.3808-0.00830.7792-0.5819-0.91280.05430.28050.087-0.05150.8271-0.0670.996726.1666-12.859111.3652
140.21440.04930.16320.0935-0.0433-0.00970.0772-0.5059-1.024-0.31840.1118-0.48171.1929-0.1457-0.00011.4098-0.10870.08330.95890.07361.321125.5052-52.619890.6504
15-0.0976-0.1468-0.047-0.08720.27290.0993-0.5537-0.07320.23440.74590.1978-0.1528-0.9880.8233-0.00021.14-0.3642-0.04691.23040.15131.049646.5274.0556116.5049
160.7890.43480.27870.64890.1960.71680.0001-0.07380.0702-0.2669-0.12670.2088-0.5293-0.6434-0.48910.71530.4822-0.1090.92830.02170.74632.10762.770485.3947
170.7505-0.22450.45340.2017-0.13270.4654-0.09420.10160.17070.1729-0.1058-0.0988-1.24890.17420.01081.7829-0.16370.0670.70870.09870.541334.835315.834560.7184
180.04020.0651-0.0625-0.0060.02930.0275-0.03280.537-0.4835-0.0161-0.19280.0534-0.26730.2885-0.00011.8561-0.0549-0.10170.93920.07840.976726.5494-11.302557.5843
190.23550.14780.2220.2175-0.12750.25760.3785-0.1573-0.102-0.1782-0.0329-0.2480.5424-0.2562-0.00041.1446-0.279-0.1610.9211-0.07141.3768.9699-48.999978.012
202.60790.7113-0.6687-0.0306-0.5062-0.0409-0.37180.5314-0.3947-0.5375-0.00780.4652-0.9462-0.3514-0.0841.72110.4057-0.29160.88070.13490.951215.236411.77553.5566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((CHAIN B AND (RESID 1028:1374 OR RESID 1451:1491)) OR (CHAIN E) OR (CHAIN F) OR (CHAIN E AND (RESID 1021:1021)))
2X-RAY DIFFRACTION2((CHAIN B AND (RESID 417:544 OR RESID 580:608)))
3X-RAY DIFFRACTION3((CHAIN B AND (RESID 545:579)))
4X-RAY DIFFRACTION4((CHAIN B AND (RESID 1375:1450)))
5X-RAY DIFFRACTION5((CHAIN B AND (RESID 1002:1027)) OR (CHAIN B AND (RESID 609:644)))
6X-RAY DIFFRACTION6((CHAIN D AND (RESID 1028:1374 OR RESID 1451:1491)))
7X-RAY DIFFRACTION7((CHAIN D AND (RESID 416:544 OR RESID 580:608)))
8X-RAY DIFFRACTION8((CHAIN D AND (RESID 545:579)))
9X-RAY DIFFRACTION9((CHAIN D AND (RESID 1375:1450)))
10X-RAY DIFFRACTION10((CHAIN D AND (RESID 1002:1027)) OR (CHAIN D AND (RESID 609:644)))
11X-RAY DIFFRACTION11((CHAIN S AND (RESID 1028:1374 OR RESID 1451:1490)) OR (CHAIN V) OR (CHAIN W) OR (CHAIN W AND (RESID 1020:1020)))
12X-RAY DIFFRACTION12((CHAIN S AND (RESID 416:544 OR RESID 580:608)))
13X-RAY DIFFRACTION13((CHAIN S AND (RESID 545:579)))
14X-RAY DIFFRACTION14((CHAIN S AND (RESID 1375:1450)))
15X-RAY DIFFRACTION15((CHAIN S AND (RESID 1002:1027)) OR (CHAIN S AND (RESID 609:640)))
16X-RAY DIFFRACTION16((CHAIN U AND (RESID 1028:1374 OR RESID 1451:1490)))
17X-RAY DIFFRACTION17((CHAIN U AND (RESID 417:544 OR RESID 580:608)))
18X-RAY DIFFRACTION18((CHAIN U AND (RESID 545:579)))
19X-RAY DIFFRACTION19((CHAIN U AND (RESID 1375:1450)))
20X-RAY DIFFRACTION20((CHAIN U AND (RESID 1002:1027)) OR (CHAIN U AND (RESID 609:644)))

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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