[English] 日本語
Yorodumi
- PDB-6eng: Crystal structure of the 43K ATPase domain of Escherichia coli gy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eng
TitleCrystal structure of the 43K ATPase domain of Escherichia coli 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 type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / 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 ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / 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 / : / PHOSPHATE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA gyrase subunit B
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,46915
Polymers87,4792
Non-polymers1,99013
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-34 kcal/mol
Surface area35700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.830, 128.070, 159.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA gyrase subunit B / Type IIA topoisomerase subunit GyrB


Mass: 43739.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENT: 43K ATPASE DOMAIN / Source: (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AES6, EC: 5.99.1.3

-
Non-polymers , 7 types, 403 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-BHW / Coumermycin A1


Mass: 1110.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H59N5O20
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG 3350, 0.2M NaH2PO4, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2015
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 2.3→33.67 Å / Num. obs: 43688 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.258 % / Biso Wilson estimate: 59.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.138 / Χ2: 0.997 / Net I/σ(I): 9.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.435.2311.2630.9861540.6981.40486.5
2.43-2.66.3710.7141.966250.9080.77798.7
2.6-2.816.6790.4643.1262650.9580.50399.3
2.81-3.086.6040.2885.2257340.9820.31299.5
3.08-3.446.4070.15810.0352590.9930.17299.6
3.44-3.976.4420.11716.9746620.9920.12899.6
3.97-4.856.2730.08523.3739750.9950.09399.8
4.85-6.836.3150.07424.4231550.9970.08199.6
6.83-33.675.7490.03833.4218590.9990.04299.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EI1

1ei1


Resolution: 2.3→33.67 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.9105 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.294 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 2180 5 %RANDOM
Rwork0.1997 ---
obs0.2025 43589 97.73 %-
Displacement parametersBiso max: 200.89 Å2 / Biso mean: 65.03 Å2 / Biso min: 32.68 Å2
Baniso -1Baniso -2Baniso -3
1-16.2642 Å20 Å20 Å2
2---1.5311 Å20 Å2
3----14.7331 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: final / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5821 0 124 390 6335
Biso mean--75.52 61.08 -
Num. residues----750
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2203SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes164HARMONIC2
X-RAY DIFFRACTIONt_gen_planes959HARMONIC5
X-RAY DIFFRACTIONt_it6130HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion791SEMIHARMONIC5
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_contact7102SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6130HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8306HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion18.88
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2689 130 5 %
Rwork0.2497 2471 -
all0.2508 2601 -
obs--80.14 %
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)
12.5681.5221-2.81843.42812.16412.90720.0229-0.03970.2866-0.00660.10530.0965-0.24430.0588-0.1283-0.0736-0.00350.04930.0547-0.0760.0628-7.321623.2212.3613
23.09750.64112.13983.93470.05673.0846-0.0357-0.0669-0.0184-0.28650.0877-0.2483-0.142-0.0539-0.0519-0.1454-0.02830.04590.04850.04240.00430.48538.0796-8.4818
30.32350.3934-0.27394.1705-0.16780.8227-0.03130.13570.3612-0.12650.15490.5196-0.3243-0.1545-0.1236-0.15670.0039-0.03420.08830.08510.063-9.459718.969-11.842
45.1296-0.02890.00854.4306-1.42160.4149-0.24680.44950.5337-0.45430.1461-0.5403-0.38560.37080.1008-0.1714-0.110.0386-0.09660.0882-0.00784.631319.59-13.2318
51.1716-1.3777-1.37195.6464-0.66112.3779-0.0957-0.11190.05250.057-0.1381-0.54260.103-0.06820.2338-0.21190.04960.05540.05470.07580.03935.00590.147-4.2675
64.62992.60162.67354.2584-0.52547.2838-0.0514-0.07590.1139-0.00370.1172-0.18530.53060.1651-0.0658-0.11450.00760.0145-0.0357-0.0148-0.08-8.9082-15.607-2.479
70.0350.55780.03024.09990.62791.21970.1496-0.18370.49930.2297-0.18710.08340.1194-0.21540.0375-0.1609-0.00790.04950.07340.02920.0194-11.6476-6.52684.7519
80.9712.7443-0.80151.61650.08310.5410.0030.01810.1260.27020.08120.08250.54-0.5334-0.0842-0.0042-0.152-0.0012-0.07590.07920.1434-23.217-20.10972.9084
95.021-0.7358-0.73461.556-0.1732.76590.0205-0.00760.1550.2792-0.06930.10180.2589-0.07530.0488-0.1718-0.06970.0108-0.0554-0.07020.0755-14.5288-10.59551.1911
101.8462-2.849-0.77772.60820.20771.09860.0609-0.03740.0926-0.0049-0.0730.2208-0.1736-0.11010.0121-0.18220.02310.03750.0360.1010.2848-20.1245.14341.4734
113.4405-0.20630.1180.0512-0.95723.4084-0.01350.27380.3414-0.21130.14480.24960.5433-0.5368-0.1314-0.1225-0.152-0.10370.01270.1103-0.0315-21.4562-16.5632-5.8636
120-0.2841.04430.572-2.90790.1438-0.0145-0.2647-0.0164-0.04560.07060.06810.0426-0.0665-0.0561-0.0689-0.1516-0.12070.00620.05840.0281-17.3357-27.786516.4587
131.0861.5618-2.87622.8216-0.60262.12930.0170.12830.1209-0.0626-0.0433-0.0028-0.16820.00060.0263-0.049-0.1520.03190.30280.1319-0.2888-17.449124.3115-57.7791
142.32790.9556-2.0174.09562.44571.987-0.05710.31420.08680.33760.06490.3125-0.03640.5276-0.0078-0.2198-0.02420.05820.1321-0.017-0.1012-24.859510.6959-45.2508
151.7572.91040.67936.63-2.61090.047-0.03890.11970.2064-0.00830.1674-0.3216-0.16850.3813-0.1286-0.2175-0.1520.08030.2676-0.1009-0.1313-14.486121.3507-41.4066
166.8680.46710.93094.5962.11182.2253-0.2387-0.06490.52550.29720.17940.5437-0.5360.29860.0593-0.197-0.07310.0857-0.1451-0.0281-0.013-28.500722.2913-40.6733
172.4296-0.01240.68436.8131.60643.1241-0.05060.02820.01680.0543-0.22890.30010.31530.16560.2795-0.2547-0.02360.07840.0648-0.0570.0119-29.1982.7016-49.5582
183.9166-0.985-0.40815.89091.79963.4147-0.1019-0.10010.17130.28090.1622-0.1060.4952-0.2382-0.0603-0.16540.0079-0.01330.0069-0.037-0.0354-15.0369-13.1323-51.1472
190.003-0.12270.06733.15-2.14781.5790.1344-0.00130.5203-0.322-0.12030.09990.22870.1713-0.0141-0.2194-0.05060.0190.0778-0.09380.1765-12.3919-4.0056-58.4981
202.3676-2.31710.30320.5141.298700.1372-0.31330.2334-0.02750.1853-0.05490.52750.5307-0.3225-0.12130.1426-0.0406-0.0419-0.15020.152-0.9281-16.5207-56.2758
210.96140.9158-0.66190.3929-0.056800.00910.04310.00750.03310.0091-0.0356-0.1599-0.0722-0.0181-0.10060.0912-0.03880.11640.05220.18491.094-21.2778-65.0233
221.1018-2.8207-1.69290.5260.33363.48610.0668-0.16380.1161-0.2154-0.05120.06260.09110.107-0.0157-0.29740.00590.0084-0.0352-0.06440.0233-10.1835-6.6092-53.2433
231.9792.8723-0.50252.55730.68630.00060.02780.02050.0719-0.0291-0.0361-0.1719-0.14620.08150.0083-0.2565-0.0473-0.0136-0.0374-0.1520.3005-4.45257.7391-55.3861
242.4233-2.8914-0.39370.72251.16471.0554-0.0417-0.27750.26770.14470.1348-0.19910.39730.5353-0.093-0.13830.1467-0.1520.0613-0.15190.0177-2.5214-13.7321-47.6421
252.0018-1.11481.38240.26141.27491.23470.070.41380.03370.1573-0.149-0.23490.1847-0.00230.079-0.18210.1520.0014-0.0039-0.00770.1312-6.1431-24.4741-71.6326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|12 - A|31 }A12 - 31
2X-RAY DIFFRACTION2{ A|32 - A|77 }A32 - 77
3X-RAY DIFFRACTION3{ A|78 - A|127 }A78 - 127
4X-RAY DIFFRACTION4{ A|128 - A|178 }A128 - 178
5X-RAY DIFFRACTION5{ A|179 - A|219 }A179 - 219
6X-RAY DIFFRACTION6{ A|220 - A|260 }A220 - 260
7X-RAY DIFFRACTION7{ A|261 - A|276 }A261 - 276
8X-RAY DIFFRACTION8{ A|277 - A|304 }A277 - 304
9X-RAY DIFFRACTION9{ A|315 - A|328 }A315 - 328
10X-RAY DIFFRACTION10{ A|329 - A|341 }A329 - 341
11X-RAY DIFFRACTION11{ A|342 - A|364 }A342 - 364
12X-RAY DIFFRACTION12{ A|365 - A|392 }A365 - 392
13X-RAY DIFFRACTION13{ B|15 - B|31 }B15 - 31
14X-RAY DIFFRACTION14{ B|32 - B|77 }B32 - 77
15X-RAY DIFFRACTION15{ B|78 - B|127 }B78 - 127
16X-RAY DIFFRACTION16{ B|128 - B|178 }B128 - 178
17X-RAY DIFFRACTION17{ B|179 - B|219 }B179 - 219
18X-RAY DIFFRACTION18{ B|220 - B|260 }B220 - 260
19X-RAY DIFFRACTION19{ B|261 - B|276 }B261 - 276
20X-RAY DIFFRACTION20{ B|277 - B|302 }B277 - 302
21X-RAY DIFFRACTION21{ B|303 - B|316 }B303 - 316
22X-RAY DIFFRACTION22{ B|317 - B|328 }B317 - 328
23X-RAY DIFFRACTION23{ B|329 - B|341 }B329 - 341
24X-RAY DIFFRACTION24{ B|342 - B|364 }B342 - 364
25X-RAY DIFFRACTION25{ B|365 - B|393 }B365 - 393

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more