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- PDB-7fse: Crystal Structure of T. maritima reverse gyrase with a minimal latch -

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Basic information

Entry
Database: PDB / ID: 7fse
TitleCrystal Structure of T. maritima reverse gyrase with a minimal latch
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: 2.89 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 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 1.2Jul 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 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)122,1266
Polymers121,3471
Non-polymers7785
Water30617
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)91.832, 91.832, 323.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1201-

HOH

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Components

#1: Protein Reverse gyrase


Mass: 121347.352 Da / Num. of mol.: 1 / Mutation: deletion of residues 389-459
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-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 54 microM protein in 50mM Tris/HCl, pH7.5, 500mM NaCl, 10mM MgCl2, 100 microM ZnCl2, 2mM BME mixed 1:1 with 20% PEG3350 0.2 M KNO3, 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: Jun 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→88.34 Å / Num. obs: 32090 / % possible obs: 99.9 % / Redundancy: 14.501 % / Biso Wilson estimate: 66.19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.298 / Rrim(I) all: 0.309 / Χ2: 0.736 / Net I/σ(I): 7.86 / Num. measured all: 465336 / Scaling rejects: 223
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
2.89-2.9714.9624.9170.5534816232923270.2625.0999.9
2.97-3.0514.8124.1850.732971222622260.2984.334100
3.05-3.1314.2263.1090.9531397220722070.3743.225100
3.13-3.2313.9112.3861.3129880214821480.5192.477100
3.23-3.3414.4171.8571.8229929207620760.71.926100
3.34-3.4515.4461.4232.5831324202920280.8331.472100
3.45-3.5815.4031.1123.4429881194019400.8871.151100
3.58-3.7315.2520.8014.728826189018900.920.829100
3.73-3.915.0610.6495.8827140180218020.9510.673100
3.9-4.0914.8480.4897.4925925174717460.9680.50699.9
4.09-4.3114.5330.3649.6924052165516550.9810.377100
4.31-4.5713.6250.25712.1821445157715740.9910.26799.8
4.57-4.8813.4870.21413.9420041148714860.9910.22299.9
4.88-5.2814.8330.19115.220529138513840.9940.19899.9
5.28-5.7815.080.19614.8219484129412920.9920.20399.8
5.78-6.4614.7530.17715.7617497118711860.9930.18399.9
6.46-7.4614.140.13518.3614691104210390.9960.1499.7
7.46-9.1412.3470.07925.73112239109090.9980.08399.9
9.14-12.9212.5270.05533.1191827347330.9990.05799.9
12.92-55.6211.5450.05333.2251034474420.9960.05698.9

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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: 2.89→55.62 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 1231 4.93 %RANDOM
Rwork0.2128 23756 --
obs0.2154 24987 78.19 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.16 Å2 / Biso mean: 70.7798 Å2 / Biso min: 30.9 Å2
Refinement stepCycle: final / Resolution: 2.89→55.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8521 0 23 17 8561
Biso mean--70.71 42.23 -
Num. residues----1040
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.010.3679180.346435136911
3.01-3.150.3692600.34791211127137
3.15-3.310.3751150.29912405252073
3.31-3.520.34311570.27072923308088
3.52-3.790.29191660.23833127329393
3.79-4.170.28791570.21723314347198
4.17-4.780.22161940.182733633557100
4.78-6.020.2631810.205634143595100
6.02-55.620.22011830.177836483831100
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)
11.00970.3596-0.05210.6427-0.39130.57010.05180.2227-0.0497-0.1382-0.1869-0.138-0.00950.1343-0.00010.64180.07010.18020.46510.05930.5234-5.187265.91869.2743
21.778-0.4870.51611.0111-0.48240.6591-0.1468-0.7518-0.78570.2902-0.5022-0.5870.28950.9049-0.00450.78990.18970.16571.28910.38491.138316.005243.373116.2425
31.6526-0.0997-0.0193.67980.8952.02980.07670.1214-0.0780.10010.0548-0.1460.08140.22360.00020.50270.06110.05040.4259-0.00080.4174-12.734217.390513.6105
40.9581-0.0446-0.1071.3608-0.07450.92080.0788-0.061-0.03870.0742-0.00540.2175-0.062-0.264-00.43040.082-0.01350.4730.04250.3769-36.995648.756129.1415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 2 through 90 ) or (resid 1101))A0
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 252 )A91 - 252
3X-RAY DIFFRACTION3chain 'A' and ((resid 253 through 456 ) or (resid 1103))A0
4X-RAY DIFFRACTION4chain 'A' and ((resid 457 through 1041 ) or (resid 1102))A0

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