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- PDB-6fqv: 2.60A BINARY COMPLEX OF S.AUREUS GYRASE with UNCLEAVED DNA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6fqv
Title2.60A BINARY COMPLEX OF S.AUREUS GYRASE with UNCLEAVED DNA
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
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
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 ...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
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: 2.6 Å
AuthorsBax, B.D. / Germe, T. / Basque, E. / Maxwell, A.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative Joint Undertaking115583
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance.
Authors: Germe, T. / Voros, J. / Jeannot, F. / Taillier, T. / Stavenger, R.A. / Bacque, E. / Maxwell, A. / Bax, B.D.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,42727
Polymers337,17612
Non-polymers1,25115
Water8,431468
1
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(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,05211
Polymers168,5886
Non-polymers4645
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20520 Å2
ΔGint-125 kcal/mol
Surface area56100 Å2
MethodPISA
2
R: DNA gyrase subunit A
S: DNA gyrase subunit B,DNA gyrase subunit B
T: DNA gyrase subunit A
U: DNA gyrase subunit B,DNA gyrase subunit B
V: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
W: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,37516
Polymers168,5886
Non-polymers78710
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21980 Å2
ΔGint-137 kcal/mol
Surface area56530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.280, 124.640, 155.240
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA gyrase subunit ... , 2 types, 8 molecules ACRTBDSU

#1: Protein
DNA gyrase subunit A


Mass: 55537.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
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: 22605.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3

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DNA chain , 1 types, 4 molecules EFVW

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


Mass: 6150.966 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 483 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.9
Details: Complex made as 13uls of protein (24mgs/ml in 20mM HEPES, 100mM Na2SO4, 5mM MnCl2, pH 7.0) + 1.5ul of 40mM MgCl2 in 15% glycerol, 3ul of DNA (2mM duplex = 4mM monomer in water) + 2uls of 50% ...Details: Complex made as 13uls of protein (24mgs/ml in 20mM HEPES, 100mM Na2SO4, 5mM MnCl2, pH 7.0) + 1.5ul of 40mM MgCl2 in 15% glycerol, 3ul of DNA (2mM duplex = 4mM monomer in water) + 2uls of 50% glycerol. Crystallisation buffer 9% PEG 5000mme, 80mM BisTris 5.9. 0.7ul complex + 0.8ul crystallisation buffer. CRYO:20% glycerol + 10.8% PEG 5000MME, 60mM BisTris 5.9,.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 107487 / % possible obs: 99.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 68.55 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5291 / CC1/2: 0.527 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CDR

5cdr


Resolution: 2.6→19.91 Å / Cor.coef. Fo:Fc: 0.9325 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.65 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.592 / SU Rfree Blow DPI: 0.277 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 5247 4.88 %RANDOM
Rwork0.1996 ---
obs0.2014 107487 99.16 %-
Displacement parametersBiso mean: 63 Å2
Baniso -1Baniso -2Baniso -3
1--5.8475 Å20 Å25.481 Å2
2---0.7499 Å20 Å2
3---6.5974 Å2
Refine analyzeLuzzati coordinate error obs: 0.386 Å
Refinement stepCycle: 1 / Resolution: 2.6→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21067 1567 78 468 23180
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00923193HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0331672HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8217SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes600HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3224HARMONIC5
X-RAY DIFFRACTIONt_it23193HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3097SEMIHARMONIC5
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_contact26524SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2618 389 4.9 %
Rwork0.2415 7545 -
all0.2425 7934 -
obs--99.16 %
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)
12.81071.22440.60952.51521.062.56390.025-0.2810.34530.0453-0.30250.6894-0.0103-0.53050.2775-0.07380.08220.0049-0.2221-0.06530.082919.489170.635780.8362
21.92320.19410.07670.6895-0.11361.20980.01050.2746-0.0444-0.0451-0.0216-0.0972-0.001-0.02160.0111-0.06820.02270.0041-0.1138-0.0254-0.064329.522137.386855.6466
32.60960.2726-0.1391.4383-1.6864-0.05310.03390.3577-0.1542-0.0175-0.01320.04670.0588-0.2362-0.0207-0.0107-0.04360.16660.1701-0.05370.040956.398640.061537.6344
44.19320.77290.38830.41470.13784.1820.06110.33610.01070.0641-0.0517-0.3609-0.26040.1988-0.0093-0.09760.00110.18150.0086-0.00630.01775.945846.539544.72
52.9931-0.69482.668402.05733.75030.04880.01790.2017-0.5368-0.25390.301-0.3242-0.2180.2050.03980.0595-0.1119-0.1540.02460.123812.978764.047560.7785
62.66511.39230.54461.61350.32323.25120.3761-0.4630.06880.3055-0.24260.11390.306-0.7965-0.1335-0.0277-0.131-0.0281-0.06450.0644-0.105226.843920.504893.9559
70.7983-0.28760.27040.84760.18831.0345-0.0067-0.12340.02620.0938-0.074-0.0419-0.07590.20940.08070.0015-0.02410.0154-0.10830.0167-0.066455.261653.143894.9752
80.2219-1.1377-1.13022.7122-1.16361.46240.0196-0.1099-0.09080.1988-0.0049-0.0389-0.01750.281-0.0147-0.1472-0.06170.10620.12340.0210.03983.110247.973678.851
93.012-0.66460.77040-0.53277.01550.12210.126-0.1026-0.2527-0.068-0.0702-0.29330.5027-0.0541-0.13510.00910.2154-0.00660.01590.046585.142240.768158.329
100.2689-0.94683.87546.00670.2362.21350.0854-0.2510.03440.1751-0.109-0.1620.28560.05020.02360.0694-0.1696-0.0927-0.02950.0292-0.234242.150826.6077107.9563
114.2388-2.6123-2.06384.91784.6845.6387-0.0313-0.7305-0.46970.633-0.11870.24540.1805-0.41280.15-0.3399-0.0512-0.0085-0.15120.1249-0.124116.691947.495972.8473
123.22822.03380.03584.13720.30890.76170.10520.25990.0885-0.2160.12010.4281-0.299-0.7207-0.2253-0.08230.01020.04220.0178-0.0191-0.315233.768943.574899.4664
133.7476-0.9414-0.95884.4405-0.14745.76110.1801-0.6359-0.6970.2070.27680.52150.3871-0.7219-0.4569-0.1087-0.0703-0.0732-0.05830.14040.10735.382119.134771.1089
142.73441.5050.47970-0.11840.35580.0241-0.12840.25120.24670.1060.5132-0.6618-0.809-0.13010.37240.15150.1582-0.0840.0920.05331.934971.3066108.9805
150.86670.55250.20433.39991.62612.6362-0.0441-0.23620.00350.145-0.24590.39010.0075-0.18140.2901-0.0930.03560.0159-0.1324-0.05350.053856.430169.737154.4781
160.99950.07740.17940.76290.0830.8294-0.02990.19470.0112-0.2445-0.04580.0362-0.00490.04610.0757-0.03460.0160.0037-0.1025-0.0106-0.054371.221935.7857132.0866
172.23522.1551-0.04822.42460.73970.49810.02010.2970.0342-0.1448-0.0096-0.03540.00930.0259-0.01050.0182-0.10260.21480.17760.05240.033499.339840.0157116.5021
187.52472.74740.31912.8150.58883.7686-0.05990.58490.1348-0.1263-0.0099-0.3496-0.11490.58180.0698-0.2725-0.07470.16240.03360.14560.2031117.959247.8574125.7361
19-0.9792-0.60965.08060-0.47315.2690.018-0.00120.1109-0.3252-0.10150.4864-0.1766-0.22790.0835-0.05750.0543-0.0824-0.1246-0.08110.034649.587861.6612133.175
200.86970.66870.65671.99311.16581.61110.2119-0.01470.06550.1418-0.27170.36090.2541-0.41490.05980.0236-0.07570.0598-0.069-0.01-0.005964.500621.0654171.438
210.6716-0.0827-0.14011.44610.26810.71770.0195-0.09140.03490.1888-0.1077-0.0991-0.03380.14920.0882-0.0645-0.05240.0252-0.11870.0338-0.023491.13454.7193173.4841
224.6654-2.7812-1.002702.62812.70230.048-0.2917-0.05740.2707-0.0866-0.1316-0.20070.31780.0386-0.1479-0.06670.1247-0.14760.02430.412120.390750.2931160.5586
232.60961.761.04070.4353-0.64515.29860.02460.3266-0.0456-0.1224-0.0034-0.0413-0.07770.5237-0.0212-0.30520.03640.2088-0.0467-0.02050.2203124.817543.1769140.5754
24-0.45131.46935.36420.31081.20113.9442-0.0064-0.08360.10220.3440.0577-0.09130.2851-0.0717-0.05130.0109-0.10970.1179-0.1237-0.0459-0.065876.805228.6692189.9233
250.9213-0.36392.35220-0.26293.2340.0169-0.3819-0.09950.08720.11250.2492-0.1422-0.7051-0.1295-0.0508-0.0205-0.00850.0869-0.0364-0.063862.649645.3508161.8482
263.93351.476-0.41464.37971.61763.6364-0.0365-0.3387-0.06420.5322-0.19250.85150.5895-0.39090.229-0.0151-0.00080.1538-0.1393-0.04460.213547.118216.7659146.5347
275.0945-0.2472-1.20372.95581.51613.1168-0.162-0.0850.43070.3805-0.22960.6133-0.3697-0.39150.39160.0156-0.04330.1-0.1181-0.04720.109465.418573.9251184.0828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|419 - B|608 }
2X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|490 }
3X-RAY DIFFRACTION3{ A|370 - A|379 A|445 - A|460 }
4X-RAY DIFFRACTION4{ A|380 - A|444 }
5X-RAY DIFFRACTION5{ A|15 - A|28 B|610 - B|636 }
6X-RAY DIFFRACTION6{ D|419 - D|608 }
7X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|369 C|461 - C|490 }
8X-RAY DIFFRACTION8{ C|370 - C|379 C|445 - C|460 }
9X-RAY DIFFRACTION9{ C|380 - C|444 }
10X-RAY DIFFRACTION10{ C|14 - C|28 D|610 - D|636 }
11X-RAY DIFFRACTION11{ E|2 - E|9 F|12 - F|18 }
12X-RAY DIFFRACTION12{ E|12 - E|18 F|2 - F|9 }
13X-RAY DIFFRACTION13{ A|245 - A|327 }
14X-RAY DIFFRACTION14{ C|245 - C|327 }
15X-RAY DIFFRACTION15{ S|417 - S|608 S|639 }
16X-RAY DIFFRACTION16{ R|30 - R|244 R|328 - R|369 R|461 - R|490 }
17X-RAY DIFFRACTION17{ R|370 - R|379 R|445 - R|460 }
18X-RAY DIFFRACTION18{ R|380 - R|444 }
19X-RAY DIFFRACTION19{ S|609 - S|636 }
20X-RAY DIFFRACTION20{ U|417 - U|608 }
21X-RAY DIFFRACTION21{ T|30 - T|244 T|328 - T|369 T|461 - T|490 }
22X-RAY DIFFRACTION22{ T|370 - T|379 T|445 - T|460 }
23X-RAY DIFFRACTION23{ T|380 - T|444 }
24X-RAY DIFFRACTION24{ U|609 - U|636 }
25X-RAY DIFFRACTION25{ V|2 - V|18 W|2 - W|18 }
26X-RAY DIFFRACTION26{ R|245 - R|327 }
27X-RAY DIFFRACTION27{ T|245 - T|327 }

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