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- PDB-8ofb: Crystal Structure of T. maritima reverse gyrase with a minimal la... -

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Basic information

Entry
Database: PDB / ID: 8ofb
TitleCrystal Structure of T. maritima reverse gyrase with a minimal latch, hexagonal form
ComponentsReverse gyrase
KeywordsHYDROLASE / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE
Function / homology
Function and homology information


reverse gyrase activity / Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / 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 domain / DEAD/DEAH box helicase / 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: 2.39 Å
AuthorsKlostermeier, D. / Rasche, R. / Mhaindarkar, V. / Kummel, D. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD 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
DepositionMar 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 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.name
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 19, 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)122,31211
Polymers121,3471
Non-polymers96410
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-65 kcal/mol
Surface area46410 Å2
Unit cell
Length a, b, c (Å)90.833, 90.833, 571.878
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1268-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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)

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Non-polymers , 5 types, 120 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.17 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 54 microM protein in 50mM Tris/HCl, pH7.5, 500mM NaCl, 10mM MgCl2, 100 microM ZnCl2, 2mM BME mixed 1:1 with 0.1M Tris/HCl pH7.5, 19% PEG3350 0.29 M Ammonium Sulfate, total volume 400nL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→78.66 Å / Num. obs: 45491 / % possible obs: 94.8 % / Redundancy: 18.7 % / Biso Wilson estimate: 42.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.069 / Rrim(I) all: 0.301 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allMean I/σ(I) obs
2.39-2.5920.31.98622760.680.4492.03767.4
7.44-78.6615.50.07222740.9990.0180.07499.918.1

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Processing

Software
NameVersionClassificationNB
Aimless0.7.9data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.39→75.85 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 2275 5.03 %RANDOM
Rwork0.2432 42919 --
obs0.2447 45194 79.36 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.62 Å2 / Biso mean: 64.3624 Å2 / Biso min: 16.02 Å2
Refinement stepCycle: final / Resolution: 2.39→75.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8521 0 48 110 8679
Biso mean--76.05 40.31 -
Num. residues----1040
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.440.214840.325981023
2.45-2.50.3241210.318840042112
2.5-2.560.3993560.34131009106531
2.56-2.630.3317770.3461723180052
2.63-2.710.38051410.35012370251172
2.71-2.80.3331690.32873076324593
2.8-2.90.38591740.31453299347399
2.9-3.020.31311530.301433483501100
3.02-3.150.34091720.301433483520100
3.15-3.320.32082020.285732913493100
3.32-3.530.29561840.261233783562100
3.53-3.80.25381750.225233993574100
3.8-4.180.25971790.209534003579100
4.18-4.790.21051870.182434643651100
4.79-6.030.24141960.213335063702100
6.03-75.850.21781850.215938103995100
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)
12.07630.39611.29483.075-0.51394.8713-0.21970.6308-0.1371-1.67940.085-0.29490.1497-0.14740.05571.27710.00930.21660.7750.10150.38950.0981-20.9968-38.4398
24.9598-3.5343-4.59769.03634.37316.1017-0.57080.3755-1.221-0.61170.1190.0191.3293-0.2580.3611.0008-0.27330.00160.86110.08650.5196-8.5919-35.1192-28.8629
32.30780.1707-0.00944.2102-0.86323.4137-0.0060.03980.013-0.40590.26550.78530.1228-0.6098-0.14190.2665-0.1478-0.12820.38670.1060.3098-37.8374-14.4813-16.227
45.2174-4.05791.29843.3387-1.28570.42030.27550.63130.2284-0.5463-0.4256-0.2176-0.00180.29850.16430.3504-0.0301-0.00620.32480.0760.2493-12.4267-14.4885-18.9208
51.9533-0.93640.53911.5731-0.38592.07350.02060.28070.0982-0.2039-0.097-0.41910.10390.39940.05850.2043-0.02370.02770.2970.09840.372410.4522-24.8047-5.4537
63.1780.1152-2.99590.27220.54613.0196-0.1624-0.69080.09570.35670.148-0.00990.3270.42880.05970.69670.2484-0.13260.62740.06790.311-1.8801-35.761133.7982
70.9252-0.0374-0.53640.64470.63922.3929-0.1157-0.21580.01460.28370.135-0.03440.24640.0114-0.01430.29690.0544-0.03450.15830.02510.1274-16.3556-22.251921.3058
83.02561.0827-0.90894.3803-1.39883.1184-0.3111-0.31210.15390.48420.2224-0.676-0.00020.5840.08980.3840.1376-0.07940.3714-0.09770.385313.4879-29.33616.7768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 225 )A2 - 225
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 286 )A226 - 286
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 456 )A287 - 456
4X-RAY DIFFRACTION4chain 'A' and (resid 457 through 526 )A457 - 526
5X-RAY DIFFRACTION5chain 'A' and (resid 527 through 683 )A527 - 683
6X-RAY DIFFRACTION6chain 'A' and (resid 684 through 735 )A684 - 735
7X-RAY DIFFRACTION7chain 'A' and (resid 736 through 953 )A736 - 953
8X-RAY DIFFRACTION8chain 'A' and (resid 954 through 1041 )A954 - 1041

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