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- PDB-7fsf: CRYSTAL STRUCTURE OF T. MARITIMA REVERSE GYRASE ACTIVE SITE VARIA... -

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Basic information

Entry
Database: PDB / ID: 7fsf
TitleCRYSTAL STRUCTURE OF T. MARITIMA REVERSE GYRASE ACTIVE SITE VARIANT Y851F
ComponentsReverse gyrase
KeywordsHydrolase / Isomerase / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE
Function / homology
Function and homology information


Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / reverse gyrase activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA unwinding involved in DNA replication / DNA topological change / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Reverse gyrase, zinc finger / Reverse gyrase zinc finger / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central ...Reverse gyrase, zinc finger / Reverse gyrase zinc finger / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsRasche, R. / Kummel, D. / Rudolph, M.G. / Klostermeier, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche Switzerland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain.
Authors: Mhaindarkar, V.P. / Rasche, R. / Kummel, D. / Rudolph, M.G. / Klostermeier, D.
History
DepositionJan 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse gyrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5933
Polymers128,4631
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.930, 103.260, 95.670
Angle α, β, γ (deg.)90.000, 116.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Reverse gyrase /


Mass: 128462.594 Da / Num. of mol.: 1 / Mutation: Y851F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: rgy, topR, TM_0173 / Production host: Escherichia coli (E. coli)
References: UniProt: O51934, DNA helicase, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 165 microM protein in 50mM Tris/HCl, pH7.5, 500mM NaCl, 10mM MgCl2, 100 microM ZnCl2, 2mM BME mixed 1:1 with 0.1M HEPES/NaOH pH 7.0, 30% Jeffamine ED-2001, total volume 200nL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: EIGER 16M / Detector: PIXEL / Date: May 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→85.38 Å / Num. obs: 40789 / % possible obs: 99.7 % / Redundancy: 11.592 % / Biso Wilson estimate: 66.33 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.351 / Rrim(I) all: 0.367 / Χ2: 0.688 / Net I/σ(I): 4.68 / Num. measured all: 472832
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.77-2.8411.9965.9210.4835867299329900.1796.18299.9
2.84-2.9211.9814.6770.6435128294229320.2244.88499.7
2.92-311.8883.8910.8234262288628820.3154.06499.9
3-3.111.7622.9671.0932123273827310.4373.10199.7
3.1-3.211.5592.3021.4131035269226850.5452.40899.7
3.2-3.3111.1781.8641.7628682257025660.651.95399.8
3.31-3.4311.3991.3112.528839253625300.7991.37299.8
3.43-3.5711.931.0323.2428643240424010.8611.07899.9
3.57-3.7311.7140.7654.1727130231723160.9110.8100
3.73-3.9211.4730.6074.9325401222822140.9450.63599.4
3.92-4.1311.4990.4316.3324481213121290.970.45199.9
4.13-4.3811.6270.3337.8422916197419710.9790.34899.8
4.38-4.6811.2890.278.7321224188718800.9850.28399.6
4.68-5.0611.0240.2449.2819391176717590.9850.25699.5
5.06-5.5411.8890.2579.1719094161016060.9830.26999.8
5.54-6.1911.8690.2429.3317412147214670.9870.25399.7
6.19-7.1511.4510.20410.1114680128612820.9860.21499.7
7.15-8.7610.8140.14312.7112004111511100.9920.15199.6
8.76-12.3810.8860.10416.3492538558500.9950.10999.4
12.38-51.8610.7930.10516.3852674984880.9920.11198

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ddu

4ddu


Resolution: 2.77→51.86 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 1475 4.98 %RANDOM
Rwork0.2191 28132 --
obs0.2219 29607 72.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.07 Å2 / Biso mean: 77.8057 Å2 / Biso min: 29.47 Å2
Refinement stepCycle: final / Resolution: 2.77→51.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9029 0 2 0 9031
Biso mean--74.87 --
Num. residues----1102
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.77-2.860.4761130.3421942076
2.86-2.960.3611400.343286890825
2.97-3.080.3603680.31831436150441
3.08-3.220.3824890.31252115220460
3.22-3.390.3651450.27952644278976
3.39-3.610.35031730.25283254342793
3.61-3.880.29121670.225635183685100
3.89-4.280.28441860.20235173703100
4.28-4.890.22481930.176234743667100
4.89-6.160.26521980.212435393737100
6.16-51.860.23112030.204935733776100
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)
11.1679-0.1591-0.25282.5861-0.78573.5068-0.0653-0.3798-0.54630.2026-0.0462-0.19170.67630.0306-0.08820.7130.0225-0.1720.40860.14260.8073-6.9904-17.0995-32.6844
24.66866.1809-1.9738.1607-2.38156.68670.0104-0.1307-0.6358-0.10450.2548-1.0060.57891.352-0.10790.71360.3004-0.23510.90610.1360.792910.4345-9.527-27.4732
31.1331-0.5886-0.31931.72131.26322.8316-0.204-0.6559-0.33740.19110.18730.2574-0.27770.282-0.20920.6215-0.018-0.12240.71580.16550.5354-9.921712.2516-10.0575
47.72214.4333-3.49855.422-2.97793.5842-0.1593-0.64760.0825-0.07830.0602-0.3907-0.02130.4896-0.03850.82790.0155-0.18380.6878-0.08090.5366-0.572425.1717-7.4876
51.2218-1.1095-0.80392.95612.10324.45830.025-0.3705-0.04990.4044-0.03120.48650.143-0.34810.10530.53580.0571-0.12090.40090.12450.4057-17.346516.4306-17.2433
60.6946-0.2588-0.13941.8295-0.3190.81150.11570.0475-0.1114-0.2853-0.0971-0.21570.06530.11730.040.5805-0.0036-0.13470.37980.00340.5246-3.458415.7469-52.8302
70.8188-1.0536-0.03363.165-0.34220.4665-0.0623-0.22420.27-0.04220.075-0.1706-0.04190.10860.03230.5597-0.0146-0.20160.359-0.04840.5366-8.501144.8612-41.7325
85.70494.2657-0.67216.1181-1.86841.37760.08290.52190.1623-0.47850.1004-0.0291-0.1805-0.0293-0.18110.78950.1844-0.01680.3712-0.00350.4736-2.612828.2091-67.1537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 2 through 194 ) or (resid 1202))A0
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 251 )A195 - 251
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 331 )A252 - 331
4X-RAY DIFFRACTION4chain 'A' and (resid 332 through 455 )A332 - 455
5X-RAY DIFFRACTION5chain 'A' and (resid 456 through 549 )A456 - 549
6X-RAY DIFFRACTION6chain 'A' and ((resid 550 through 790 ) or (resid 1201))A0
7X-RAY DIFFRACTION7chain 'A' and (resid 791 through 1013 )A791 - 1013
8X-RAY DIFFRACTION8chain 'A' and (resid 1014 through 1103 )A0

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