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- PDB-6enh: Crystal structure of the 43K ATPase domain of Thermus thermophilu... -

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Basic information

Entry
Database: PDB / ID: 6enh
TitleCrystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with an aminocoumarin
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / TOPOISOMERASE / GYRASE B-AMINOCOUMARIN COMPLEX
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. ...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 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 / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Coumermycin A1 / IMIDAZOLE / DNA gyrase subunit B
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsVanden Broeck, A. / McEwen, A.G. / Lamour, V.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structural Basis for DNA Gyrase Interaction with Coumermycin A1.
Authors: Vanden Broeck, A. / McEwen, A.G. / Chebaro, Y. / Potier, N. / Lamour, V.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2494
Polymers43,0011
Non-polymers1,2483
Water1,62190
1
A: DNA gyrase subunit B
hetero molecules

A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4988
Polymers86,0022
Non-polymers2,4966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)166.370, 37.850, 66.750
Angle α, β, γ (deg.)90.000, 110.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA gyrase subunit B /


Mass: 43000.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FRAGMENT: 43K ATPASE DOMAIN
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: gyrB, TTHA1586 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHZ4, EC: 5.99.1.3
#2: Chemical ChemComp-BHW / Coumermycin A1 / Coumermycin A1


Mass: 1110.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H59N5O20
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 47% MPD, 0.1M Imidazole pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 5, 2015
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 1.94→23.85 Å / Num. obs: 28248 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.73 % / Biso Wilson estimate: 60.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rrim(I) all: 0.025 / Χ2: 1.012 / Net I/σ(I): 18.97 / Num. measured all: 77129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.94-2.062.6910.8171.0245530.6091.01296.6
2.06-2.22.6290.4132.0943160.8490.51396.8
2.2-2.372.7290.1964.4540030.960.24296.8
2.37-2.62.7510.1078.2736870.9860.13296.9
2.6-2.92.7990.05316.0133540.9960.06596.4
2.9-3.352.8020.02830.5529130.9990.03595.1
3.35-4.12.8060.01652.824490.9990.01993.7
4.1-5.792.7250.01265.95189510.01592.3
5.79-23.852.6680.01571.2510780.9990.01890.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KIJ

1kij


Resolution: 1.94→23.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.9536 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1410 5 %RANDOM
Rwork0.1972 ---
obs0.199 28205 96.08 %-
Displacement parametersBiso max: 198.85 Å2 / Biso mean: 79.85 Å2 / Biso min: 45.76 Å2
Baniso -1Baniso -2Baniso -3
1-5.541 Å20 Å2-3.9026 Å2
2---0.2346 Å20 Å2
3----5.3064 Å2
Refine analyzeLuzzati coordinate error obs: 0.301 Å
Refinement stepCycle: final / Resolution: 1.94→23.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 90 90 3008
Biso mean--81.72 74.4 -
Num. residues----366
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1044SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes500HARMONIC5
X-RAY DIFFRACTIONt_it2977HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion368SEMIHARMONIC5
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_contact3285SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2977HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4036HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion18.95
LS refinement shellResolution: 1.94→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3096 150 4.97 %
Rwork0.2534 2868 -
all0.2563 3018 -
obs--98.14 %
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)
1-0.74521.88890.35876.25393.28983.5357-0.1292-0.14180.45010.2061-0.0341-0.0945-0.05090.00750.1633-0.21340.0289-0.1158-0.2573-0.06160.1067-31.6608-3.415652.8281
23.49381.09260.74691.7763-0.19135.54010.07330.3224-0.34170.05810.0437-0.35640.45860.6989-0.1169-0.18610.0562-0.01750.019-0.0067-0.0508-31.5649-20.495639.3335
35.96073.2951-1.19112.1494-0.98973.32250.01660.32240.48520.2692-0.0626-0.4808-0.39660.69890.046-0.1755-0.0548-0.08620.03410.07470.1933-20.5498-9.203645.2794
47.6813-0.35721.57381.70420.19384.44360.16910.3224-0.46380.3582-0.0945-0.4480.47470.6989-0.0746-0.15440.0812-0.0921-0.05040.04110.0266-21.6846-20.594148.12
52.77560.8620.51173.09990.06213.41310.09140.5454-0.41620.08180.12070.12030.66290.0941-0.2122-0.05820.0328-0.06830.0544-0.0958-0.0595-38.9157-26.536736.7393
67.05260.96972.92097.6351.30351.7603-0.01040.22780.13290.14250.1942-0.3706-0.08250.664-0.1838-0.1035-0.10310.0950.2911-0.0384-0.2558-44.4631-20.354516.097
7-1.1977-0.36951.49873.21090.23354.25660.0699-0.5030.17930.47130.26340.295-0.40350.3693-0.3333-0.1624-0.10450.10150.304-0.1559-0.2484-48.4772-13.427623.7171
89.5001-1.6225-1.01580.3371-3.56255.11160.23130.53330.6653-0.4251-0.1999-0.3623-0.36640.1268-0.03140.0961-0.18750.1734-0.08820.0692-0.2305-49.3483-9.89395.7802
94.1425-2.3468-2.70522.5959-1.67313.15440.1361-0.32250.2614-0.1657-0.04850.144-0.37540.3477-0.0877-0.0718-0.13890.0497-0.0049-0.0627-0.2178-49.8063-10.072313.7355
104.18452.72664.4534.4318-0.0552.71580.00680.30110.4914-0.2027-0.3472-0.5921-0.02840.62710.3403-0.1529-0.19520.15790.3040.09-0.0675-41.3483-8.289812.8685
114.598-0.09351.79933.02661.5750.7038-0.17050.2270.1729-0.6135-0.14050.3111-0.08460.40240.31090.12910.1511-0.04820.0182-0.0569-0.2262-64.4488-15.9742.8479
12-0.19551.53342.739102.65652.35230.05660.0061-0.03580.0040.1202-0.01640.01550.0146-0.1767-0.37430.02320.03880.304-0.08480.0029-11.6137-13.996231.3008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|6 - A|28 }A6 - 28
2X-RAY DIFFRACTION2{ A|29 - A|73 }A29 - 73
3X-RAY DIFFRACTION3{ A|74 - A|124 }A74 - 124
4X-RAY DIFFRACTION4{ A|125 - A|176 }A125 - 176
5X-RAY DIFFRACTION5{ A|177 - A|217 }A177 - 217
6X-RAY DIFFRACTION6{ A|218 - A|258 }A218 - 258
7X-RAY DIFFRACTION7{ A|259 - A|274 }A259 - 274
8X-RAY DIFFRACTION8{ A|275 - A|303 }A275 - 303
9X-RAY DIFFRACTION9{ A|304 - A|329 }A304 - 329
10X-RAY DIFFRACTION10{ A|330 - A|362 }A330 - 362
11X-RAY DIFFRACTION11{ A|363 - A|390 }A363 - 390
12X-RAY DIFFRACTION12{ A|401 - A|401 }A401

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