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- PDB-5cdr: 2.65 structure of S.aureus DNA gyrase and artificially nicked DNA -

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Basic information

Entry
Database: PDB / ID: 5cdr
Title2.65 structure of S.aureus DNA gyrase and artificially nicked DNA
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3')
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
  • DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE
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
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 / 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 ...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 / 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 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 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: 2.65 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)165,43916
Polymers164,7227
Non-polymers7179
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21920 Å2
ΔGint-121 kcal/mol
Surface area57470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.395, 93.395, 410.583
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 ACBD

#1: Protein DNA gyrase subunit A /


Mass: 54738.453 Da / Num. of mol.: 2 / Mutation: Y123F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#2: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 21345.270 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3

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DNA chain , 3 types, 3 molecules EGF

#3: DNA chain DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3')


Mass: 2451.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 6134.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 653 molecules

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


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 150mM BisTris pH 6.2, 11% PEG 5000 MME. / PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 58268 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.01 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.025 / Net I/av σ(I): 13.521 / Net I/σ(I): 8.4 / Num. measured all: 189383
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.65-2.73.40.46329270.912100
2.7-2.743.40.43329360.95199.9
2.74-2.83.40.37628970.94199.8
2.8-2.853.40.32929410.94699.8
2.85-2.923.40.28929110.9799.9
2.92-2.983.40.23629150.94799.7
2.98-3.063.40.20729350.96899.9
3.06-3.143.40.18229101.00299.8
3.14-3.233.30.15429541.00799.7
3.23-3.343.40.12329510.98999.8
3.34-3.463.40.10528970.99899.8
3.46-3.63.40.08729491.00599.9
3.6-3.763.30.07428911.00699.7
3.76-3.963.20.06528851.02599.2
3.96-4.213.20.05829311.04699.4
4.21-4.533.10.06128681.3498.1
4.53-4.9830.06528831.68597.6
4.98-5.73.10.06529001.50198.8
5.7-7.1830.0429200.78798.5
7.18-402.80.02528670.54596.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCS

2xcs


Resolution: 2.65→39.74 Å / Cor.coef. Fo:Fc: 0.9285 / Cor.coef. Fo:Fc free: 0.9203 / SU R Cruickshank DPI: 0.609 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.615 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 2379 4.1 %RANDOM
Rwork0.1879 ---
obs0.1888 58050 99.33 %-
Displacement parametersBiso max: 139.21 Å2 / Biso mean: 49.38 Å2 / Biso min: 10.88 Å2
Baniso -1Baniso -2Baniso -3
1-3.0828 Å20 Å20 Å2
2--3.0828 Å20 Å2
3----6.1656 Å2
Refine analyzeLuzzati coordinate error obs: 0.332 Å
Refinement stepCycle: final / Resolution: 2.65→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10625 733 39 644 12041
Biso mean--78.77 45.12 -
Num. residues----1380
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4409SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes348HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1682HARMONIC5
X-RAY DIFFRACTIONt_it12056HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1581SEMIHARMONIC5
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_contact14011SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12056HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16451HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion17.95
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2542 196 4.55 %
Rwork0.223 4114 -
all0.2244 4310 -
obs--99.33 %
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)
12.80570.2858-0.94521.3336-0.18831.57890.1119-0.51630.38010.0561-0.04110.3148-0.10560.0104-0.0708-0.03570.0224-0.0323-0.0374-0.1668-0.055413.662254.081364.0002
20.99320.2337-0.07440.73480.0981.1268-0.0102-0.0166-0.14770.05480.0169-0.0008-0.0156-0.0191-0.0067-0.01370.0319-0.0236-0.1295-0.0356-0.005830.191928.838534.2676
3-1.05220.1726-0.35513.2461-0.15420.04640.00330.03520.00330.0034-0.0436-0.08210.05150.06070.04030.00280.0551-0.0082-0.192-0.0250.12729.6522-2.601240.2899
45.04581.12711.67871.7495-0.036700.0688-0.0937-0.1423-0.08390.013-0.24190.1304-0.1952-0.08180.09520.0371-0.0192-0.1931-0.0139-0.041811.8333-13.498745.7499
51.7526-1.05711.7231.94921.09892.7170.014-0.24130.0190.11980.0023-0.14780.08690.143-0.01630.00290.0172-0.0506-0.0035-0.091-0.077733.024246.67961.8496
63.169-0.3199-0.21621.5268-0.20270.8987-0.05890.45630.5457-0.0741-0.0145-0.2003-0.18510.06480.0735-0.00680.0756-0.0517-0.02020.1457-0.0914-1.101854.097716.1535
71.1948-0.1398-0.31180.2658-0.00771.0342-0.0482-0.0228-0.1427-0.0382-0.05680.0442-0.02430.0140.105-0.00980.0743-0.0203-0.1051-0.06280.0109-18.89133.507948.0064
80.24960.1971.37732.0010.6510.92810.0505-0.02160.0286-0.0059-0.02940.07190.0619-0.0542-0.0211-0.02190.03730.0377-0.243-0.14620.092-22.57882.109143.7483
94.506-0.2079-0.78482.2483-0.48560.99870.0554-0.103-0.2194-0.006-0.06760.0250.07510.1510.01230.09640.0068-0.041-0.2074-0.0727-0.032-7.2385-12.14140.5214
102.1613-0.38882.030.8397-1.00673.5508-0.0450.22290.0929-0.0620.00610.05440.0541-0.12430.03890.01420.13-0.08330.06050.013-0.0973-21.299849.403318.6792
11-0.28210.76830.14724.3220.86972.0815-0.02370.08260.134-0.1568-0.01350.0216-0.1064-0.03140.03730.0023-0.0167-0.0275-0.1548-0.0222-0.023426.311149.971841.8003
12-0.12651.270.01952.1187-0.93532.1830.0028-0.07770.17530.15970.0132-0.1079-0.19070.2065-0.0159-0.09860.1503-0.0902-0.1989-0.109-0.0808-10.048652.732239.0976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|417 - B|608 }B417 - 608
2X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|491 }A29 - 244
3X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|491 }A328 - 369
4X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|491 }A461 - 491
5X-RAY DIFFRACTION3{ A|374 - A|379 A|451 - A|460 }A374 - 379
6X-RAY DIFFRACTION3{ A|374 - A|379 A|451 - A|460 }A451 - 460
7X-RAY DIFFRACTION4{ A|380 - A|450 }A380 - 450
8X-RAY DIFFRACTION5{ A|9 - A|28 B|609 - B|640 }A9 - 28
9X-RAY DIFFRACTION5{ A|9 - A|28 B|609 - B|640 }B609 - 640
10X-RAY DIFFRACTION6{ D|417 - D|608 }D417 - 608
11X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|329 C|461 - C|490 }C29 - 244
12X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|329 C|461 - C|490 }C328 - 329
13X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|329 C|461 - C|490 }C461 - 490
14X-RAY DIFFRACTION8{ C|373 - C|379 C|451 - C|460 }C373 - 379
15X-RAY DIFFRACTION8{ C|373 - C|379 C|451 - C|460 }C451 - 460
16X-RAY DIFFRACTION9{ C|380 - C|450 }C380 - 450
17X-RAY DIFFRACTION10{ C|10 - C|28 D|609 - D|639 }C10 - 28
18X-RAY DIFFRACTION10{ C|10 - C|28 D|609 - D|639 }D609 - 639
19X-RAY DIFFRACTION11{ E|1 - E|8 F|2013 - F|2019 }E1 - 8
20X-RAY DIFFRACTION11{ E|1 - E|8 F|2013 - F|2019 }F2013 - 2019
21X-RAY DIFFRACTION12{ E|2009 - E|2020 F|2 - F|8 }E2009 - 2020
22X-RAY DIFFRACTION12{ E|2009 - E|2020 F|2 - F|8 }F2 - 8

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