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- PDB-5cdm: 2.5A structure of QPT-1 with S.aureus DNA gyrase and DNA -

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Basic information

Entry
Database: PDB / ID: 5cdm
Title2.5A structure of QPT-1 with S.aureus DNA gyrase and DNA
Components
  • (DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)- ...) x 2
  • (DNA gyrase subunit ...) x 2
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling 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
Rossmann fold - #670 / 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 / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...Rossmann fold - #670 / 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 / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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, 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-54Q / THYMIDINE-5'-MONOPHOSPHATE / : / 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: 2.5 Å
AuthorsBax, B.D. / Srikannathasan, V. / Chan, P.F.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.
Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, ...Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, C.E. / Tanner, R. / Theobald, A.J. / Stavenger, R.A. / Bax, B.D. / Gwynn, M.N.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide.
Authors: Srikannathasan, V. / Wohlkonig, A. / Shillings, A. / Singh, O. / Chan, P.F. / Huang, J. / Gwynn, M.N. / Fosberry, A.P. / Homes, P. / Hibbs, M. / Theobald, A.J. / Spitzfaden, C. / Bax, B.D.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 B
A: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
I: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
N: DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,91317
Polymers164,4298
Non-polymers1,4849
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22010 Å2
ΔGint-137 kcal/mol
Surface area56370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.884, 93.884, 412.482
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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DNA gyrase subunit ... , 2 types, 4 molecules BDAC

#1: Protein DNA gyrase subunit B,DNA gyrase subunit B


Mass: 21331.242 Da / Num. of mol.: 2
Mutation: GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED ...Mutation: GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG,GREEK KEY DOMAIN DELETED (544-579) AMD REPLACED WITH TWO RESIDUES, TG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3
#2: Protein DNA gyrase subunit A


Mass: 54777.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3

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DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)- ... , 2 types, 4 molecules EFIN

#3: DNA chain DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 2451.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*C*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 337 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-54Q / (2R,4S,4aS)-2,4-dimethyl-8-nitro-1,2,4,4a-tetrahydro-2'H,6H-spiro[1,4-oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4',6'(1'H,3'H)-trione


Mass: 374.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N4O6
#10: Chemical ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Source: (synth.) synthetic construct (others) / Comment: dTMP*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 150mM BisTris pH6.2, 11% PEG 5000 MME / PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.22
ReflectionResolution: 2.5→36.785 Å / Num. all: 67361 / Num. obs: 67361 / % possible obs: 95.4 % / Redundancy: 2.5 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.123 / Rsym value: 0.098 / Net I/av σ(I): 4.938 / Net I/σ(I): 6.7 / Num. measured all: 166459
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.642.20.4471.72103397370.3580.4471.994.5
2.64-2.82.50.32822417395750.2480.3282.997.8
2.8-2.992.60.2123.62387290200.1560.2124.398.5
2.99-3.232.60.154.92173883910.1110.155.998
3.23-3.542.50.1154.21891576060.0890.115897.3
3.54-3.952.10.0956.21368963870.0760.0959.289.7
3.95-4.562.70.0758.51614560660.0540.07511.897.2
4.56-5.592.60.078.71293450300.0510.0711.894.8
5.59-7.912.30.0589.9803334310.0440.05811.284.1
7.91-36.7852.80.0688.2592721180.0470.06813.994

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.16data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCS

2xcs


Resolution: 2.5→36.785 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.08 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1923 3499 5.19 %
Rwork0.1627 63896 -
obs0.1652 67361 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.43 Å2 / Biso mean: 54.2607 Å2 / Biso min: 20.44 Å2
Refinement stepCycle: final / Resolution: 2.5→36.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10558 772 134 328 11792
Biso mean--40.87 41.01 -
Num. residues----1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111789
X-RAY DIFFRACTIONf_angle_d1.13516087
X-RAY DIFFRACTIONf_chiral_restr0.051807
X-RAY DIFFRACTIONf_plane_restr0.0051991
X-RAY DIFFRACTIONf_dihedral_angle_d17.6054691
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5005-2.54360.30911630.2763231339491
2.5436-2.58980.28411830.28173108329188
2.5898-2.63960.28811890.2743149333890
2.6396-2.69340.32151990.27283213341291
2.6934-2.7520.28471760.24843328350494
2.752-2.81590.2481520.23983265341794
2.8159-2.88630.25831630.23173305346894
2.8863-2.96430.25771630.22123326348994
2.9643-3.05140.23182020.21023264346692
3.0514-3.14980.22241880.20383261344992
3.1498-3.26230.21311680.1873314348294
3.2623-3.39270.19291690.18083276344594
3.3927-3.54690.20261640.17063210337491
3.5469-3.73360.2161500.15523005315585
3.7336-3.9670.16641600.13893010317085
3.967-4.27250.15651700.11923304347493
4.2725-4.7010.12281770.10743231340892
4.701-5.37780.14461800.11463134331489
5.3778-6.76270.1711530.14073014316785
6.7627-29.99290.15551400.11962948308883
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)
11.3243-0.0558-0.28490.1761-0.31880.6346-0.0773-0.1670.08190.16430.03820.0817-0.1554-0.07730.05350.53850.00020.0590.3545-0.03340.253913.727551.386664.2229
21.15520.0216-0.09891.24730.38941.6739-0.014-0.33850.10260.39010.0978-0.51260.15610.06090.0610.5885-0.0502-0.05780.4362-0.01040.441834.226145.063961.411
30.9025-0.1787-0.14820.97820.12610.9207-0.02330.0455-0.18960.06-0.0191-0.0587-0.07950.02220.05040.3714-0.06290.07620.2065-0.00550.31928.867426.736134.0299
41.0079-0.1030.02150.6699-0.14730.9458-0.15160.15180.18030.4398-0.0471-0.0708-0.5617-0.1110.18180.7026-0.144-0.00520.35760.01210.36128.710154.415614.2802
51.56291.02270.10741.01560.00040.23010.02760.2097-0.0776-0.1232-0.0866-0.23890.2330.1590.0680.55270.04330.05960.24580.0360.426126.2151-6.386237.4614
61.64570.24380.25550.7022-0.69670.8720.08080.0053-0.4634-0.00280.05980.09360.5573-0.0569-0.10270.6458-0.06560.02080.23160.05070.417610.2471-16.979745.759
71.0797-0.0285-0.11450.19670.11360.81680.08050.30960.1507-0.0172-0.0191-0.0558-0.37360.0216-0.04450.6643-0.00080.10640.46880.08040.3389-3.240950.997416.0603
80.0568-0.03030.04460.1016-0.38691.7556-0.10780.5836-0.0865-0.4778-0.01250.349-0.1598-0.44780.02760.49750.0426-0.04090.53850.04920.3583-24.213946.76518.9384
90.72080.1009-0.35851.2182-0.32660.9969-0.0630.0078-0.1972-0.0998-0.06510.03290.0568-0.02110.12380.2931-0.00210.03530.20210.04320.2985-20.914129.916747.5041
101.1205-0.07480.01230.64920.18180.925-0.288-0.1950.1378-0.10830.1375-0.0942-0.3750.13810.04850.5807-0.0102-0.0380.27420.06390.3478-17.616558.970265.3003
110.5991-0.40680.08270.6168-0.01780.4611-0.0020.0479-0.121-0.25260.06050.0077-0.0674-0.0536-0.02010.5978-0.11920.03940.2691-0.0420.5124-20.4616-3.222546.6041
121.1857-0.0785-0.15470.7740.0361.0788-0.08950.1127-0.1331-0.13610.00630.0937-0.07740.06020.09280.5896-0.0667-0.03210.2542-00.4418-5.6018-15.765539.6225
131.83980.1256-0.33960.7189-0.23860.9224-0.12640.16440.1905-0.089-0.0274-0.191-0.174-0.03870.04760.416-0.10090.0370.23050.00590.370622.706648.289241.9047
142.34060.20890.62091.59030.30181.3503-0.2304-0.15150.25670.16990.13420.2618-0.254-0.1123-0.01850.46940.04350.05580.27120.06780.3886-13.723849.37338.6471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1((chain B and (resid 417:607)))B0
2X-RAY DIFFRACTION2((chain A and (resid 12:25)) or (chain B and (resid 608:638)))A0
3X-RAY DIFFRACTION3((chain A and (resid 26:244 or resid 328:369 or resid 458:490)))A26 - 244
4X-RAY DIFFRACTION3((chain A and (resid 26:244 or resid 328:369 or resid 458:490)))A328 - 369
5X-RAY DIFFRACTION3((chain A and (resid 26:244 or resid 328:369 or resid 458:490)))A458 - 490
6X-RAY DIFFRACTION4((chain A and (resid 245:327)))A0
7X-RAY DIFFRACTION5((chain A and (resid 370:379 or resid 443:457)))A370 - 379
8X-RAY DIFFRACTION5((chain A and (resid 370:379 or resid 443:457)))A443 - 457
9X-RAY DIFFRACTION6((chain A and (resid 380:442)))A0
10X-RAY DIFFRACTION7((chain D and (resid 417:608)))D0
11X-RAY DIFFRACTION8((chain C and (resid 12:25)) or (chain D and (resid 609:638)))C0
12X-RAY DIFFRACTION9((chain C and (resid 26:244 or resid 328:369 or resid 458:490)))C26 - 244
13X-RAY DIFFRACTION9((chain C and (resid 26:244 or resid 328:369 or resid 458:490)))C328 - 369
14X-RAY DIFFRACTION9((chain C and (resid 26:244 or resid 328:369 or resid 458:490)))C458 - 490
15X-RAY DIFFRACTION10((chain C and (resid 245:327)))C0
16X-RAY DIFFRACTION11((chain C and (resid 370:379 or resid 443:457)))C370 - 379
17X-RAY DIFFRACTION11((chain C and (resid 370:379 or resid 443:457)))C443 - 457
18X-RAY DIFFRACTION12((chain C and (resid 380:442)))C0
19X-RAY DIFFRACTION13((chain E and (resid 1:2010)) or (chain F and (resid 2011:2019)) or (chain I and (resid 21:21)))E0
20X-RAY DIFFRACTION14((chain E and (resid 2011:2020)) or (chain F and (resid 2:2010)) or (chain I and (resid 1:1)))E0

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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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