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- PDB-1in7: THERMOTOGA MARITIMA RUVB R170A -

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Basic information

Entry
Database: PDB / ID: 1in7
TitleTHERMOTOGA MARITIMA RUVB R170A
ComponentsHOLLIDAY JUNCTION DNA HELICASE RUVB
KeywordsDNA BINDING PROTEIN / AAA+-Class ATPase / Winged-Helix Domain / Holliday Junction / Branch Migration / DNA translocase / Walker A / Walker B / Sensor 1 / Sensor 2 / Arginine Finger
Function / homology
Function and homology information


Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvB AAA lid domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvB AAA lid domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase family associated with various cellular activities (AAA) / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Holliday junction branch migration complex subunit RuvB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPutnam, C.D. / Clancy, S.B. / Tsuruta, H. / Wetmur, J.G. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structure and mechanism of the RuvB Holliday junction branch migration motor.
Authors: Putnam, C.D. / Clancy, S.B. / Tsuruta, H. / Gonzalez, S. / Wetmur, J.G. / Tainer, J.A.
History
DepositionMay 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ACCORDING TO THE AUTHOR, THE BIOLOGICAL UNIT IS ACTUALLY A HEXAMER; HOWEVER, THE HEXAMER IS NOT REPRESENTED IN THE CRYSTAL PACKING. NON-CRYSTALLOGRAPHIC SYMMETRY OPERATIONS TO GENERATE THE HEXAMER ARE NOT AVAILABLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HOLLIDAY JUNCTION DNA HELICASE RUVB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6654
Polymers37,1201
Non-polymers5453
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.639, 86.639, 82.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein HOLLIDAY JUNCTION DNA HELICASE RUVB / RUVB


Mass: 37120.062 Da / Num. of mol.: 1 / Mutation: R170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: RuvB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q56313
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1M 1,6-hexanediol, 100 mM cobalt chloride, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 M1,6-hexanediol1reservoir
2100 mM1reservoirCoCl2
3100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 16, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. all: 31816 / Num. obs: 31816 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2723 / % possible all: 83.5
Reflection
*PLUS
Lowest resolution: 35 Å / Num. measured all: 94671
Reflection shell
*PLUS
% possible obs: 83.5 % / Rmerge(I) obs: 0.49

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IN4

1in4


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2554833.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2741 10 %RANDOM
Rwork0.216 ---
all0.219 27487 --
obs0.216 27487 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.01 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.33 Å2-0.61 Å20 Å2
2---4.33 Å20 Å2
3---8.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-3.5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 35 231 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 457 10.1 %
Rwork0.262 4084 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ADP_PAR.TXTADP_TOP.TXT
X-RAY DIFFRACTION4ACT_PAR.TXTACT_TOP.TXT
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.296 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.262

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