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- PDB-3oiy: Helicase domain of reverse gyrase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3oiy
TitleHelicase domain of reverse gyrase from Thermotoga maritima
Componentsreverse gyrase helicase domain
KeywordsISOMERASE / TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PYROPHOSPHATE 2-
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The latch modulates nucleotide and DNA binding to the helicase-like domain of Thermotoga maritima reverse gyrase and is required for positive DNA supercoiling.
Authors: Ganguly, A. / Del Toro Duany, Y. / Rudolph, M.G. / Klostermeier, D.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: reverse gyrase helicase domain
B: reverse gyrase helicase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5344
Polymers96,3232
Non-polymers2112
Water1,78399
1
A: reverse gyrase helicase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3733
Polymers48,1621
Non-polymers2112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: reverse gyrase helicase domain


Theoretical massNumber of molelcules
Total (without water)48,1621
Polymers48,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.646, 126.514, 132.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein reverse gyrase helicase domain


Mass: 48161.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growDetails: 0.2 M Magnesium formiate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→132.71 Å / Num. obs: 42547 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.34 / Rsym value: 0.659 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDS(VERSION May 10data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GKU

1gku


Resolution: 2.35→44.358 Å / SU ML: 0.38 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 1955 5.07 %
Rwork0.2084 --
obs0.2105 38558 90.43 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.82 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2688 Å2-0 Å20 Å2
2---4.9468 Å20 Å2
3---5.2156 Å2
Refinement stepCycle: LAST / Resolution: 2.35→44.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 10 99 6742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126772
X-RAY DIFFRACTIONf_angle_d1.5649093
X-RAY DIFFRACTIONf_dihedral_angle_d17.2182582
X-RAY DIFFRACTIONf_chiral_restr0.113994
X-RAY DIFFRACTIONf_plane_restr0.0061143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40880.41511270.39372083X-RAY DIFFRACTION74
2.4088-2.47390.39471140.35732232X-RAY DIFFRACTION78
2.4739-2.54670.44891230.34282308X-RAY DIFFRACTION81
2.5467-2.62890.41781350.3322407X-RAY DIFFRACTION84
2.6289-2.72290.38641270.3192379X-RAY DIFFRACTION83
2.7229-2.83190.32751410.29092514X-RAY DIFFRACTION88
2.8319-2.96070.33291300.26782662X-RAY DIFFRACTION93
2.9607-3.11680.31321550.24382764X-RAY DIFFRACTION97
3.1168-3.3120.32011560.23852812X-RAY DIFFRACTION97
3.312-3.56760.24931530.21682815X-RAY DIFFRACTION98
3.5676-3.92650.24161470.21192750X-RAY DIFFRACTION95
3.9265-4.49420.19031450.15862900X-RAY DIFFRACTION99
4.4942-5.66030.19631400.14742950X-RAY DIFFRACTION100
5.6603-44.36640.18441620.17423027X-RAY DIFFRACTION97
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)
13.1062-0.6498-0.81011.52270.07130.56310.05180.2810.00030.0375-0.0887-0.0449-0.0325-0.2820.03390.1580.0340.00980.2774-0.03280.1165-11.792818.993449.2548
21.0435-0.1829-0.79291.56960.44826.3034-0.0156-0.13840.0080.2107-0.0335-0.09550.14470.40760.040.24820.03880.01740.3848-0.06340.104417.9946.183522.4115
32.0292-0.36050.06092.00430.3643.03730.1448-0.2650.36980.03970.10660.32-0.54370.1421-0.22260.4212-0.13640.19160.2568-0.20470.3682-2.8209-21.528329.5013
42.1687-0.59520.51741.5858-0.63180.87780.1206-0.0574-0.0503-0.2175-0.07730.00580.25260.2073-0.03940.19960.05120.03260.27740.00860.031318.6463-2.802358.6046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 58:282)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 283:534)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 59:281)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 284:534)

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