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- PDB-7oa5: RUVA COMPLEXED TO A HOLLIDAY JUNCTION. -

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Basic information

Entry
Database: PDB / ID: 7oa5
TitleRUVA COMPLEXED TO A HOLLIDAY JUNCTION.
Components
  • DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*AP*GP*TP*TP*CP*GP*C)-3')
  • DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')
  • DNA (5'-D(*GP*CP*GP*AP*AP*CP*TP*CP*GP*CP*GP*AP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')
  • Holliday junction ATP-dependent DNA helicase RuvA
KeywordsDNA BINDING PROTEIN / Complex / DNA Binding
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA recombination / DNA repair / ATP binding / cytoplasm
Similarity search - Function
Bacterial DNA recombination protein RuvA / Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.378 Å
AuthorsRoe, S.M. / Pearl, L.H.
CitationJournal: Molecular Cell / Year: 1998
Title: Crystal structure of an octameric RuvA-Holliday junction complex
Authors: Roe, S.M. / Pearl, L.H.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
SupersessionNov 13, 2024ID: 1BVS
Revision 1.2Nov 13, 2024Group: Advisory / Structure summary / Category: pdbx_database_PDB_obs_spr / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Holliday junction ATP-dependent DNA helicase RuvA
B: Holliday junction ATP-dependent DNA helicase RuvA
C: Holliday junction ATP-dependent DNA helicase RuvA
D: Holliday junction ATP-dependent DNA helicase RuvA
E: Holliday junction ATP-dependent DNA helicase RuvA
F: Holliday junction ATP-dependent DNA helicase RuvA
G: Holliday junction ATP-dependent DNA helicase RuvA
H: Holliday junction ATP-dependent DNA helicase RuvA
I: DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*AP*GP*TP*TP*CP*GP*C)-3')
J: DNA (5'-D(*GP*CP*GP*AP*AP*CP*TP*CP*GP*CP*GP*AP*AP*C)-3')
K: DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')
L: DNA (5'-D(P*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,62214
Polymers184,54212
Non-polymers802
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32600 Å2
ΔGint-278 kcal/mol
Surface area65960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.35, 141.35, 106.47
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Holliday junction ATP-dependent DNA helicase RuvA


Mass: 20772.672 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (strain TN) (bacteria)
Strain: TN / Gene: ruvA, ML0482, B1177_C2_188 / Production host: Escherichia coli (E. coli) / References: UniProt: P40832, DNA helicase

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DNA chain , 4 types, 4 molecules IJKL

#2: DNA chain DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*AP*GP*TP*TP*CP*GP*C)-3')


Mass: 4600.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria)
#3: DNA chain DNA (5'-D(*GP*CP*GP*AP*AP*CP*TP*CP*GP*CP*GP*AP*AP*C)-3')


Mass: 4274.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria)
#4: DNA chain DNA (5'-D(*AP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')


Mass: 4899.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria)
#5: DNA chain DNA (5'-D(P*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*AP*CP*T)-3')


Mass: 4585.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria)

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Non-polymers , 2 types, 458 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.35 Å3/Da / Density % sol: 63 % / Description: Trigonal bipyramidal
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: CRYSTALS GROWN UNDER OIL IN TERASAKI PLATES. DROPS FORMED FROM A 1:1 MIXTURE OF PROTEIN/DNA COMPLEX (10MG/ML COMPLEX, 20MM TRIS PH 7.5, 1MM EDTA, 0.1M NACL, 15% GLYCEROL) AND 1.4M NACITRATE, ...Details: CRYSTALS GROWN UNDER OIL IN TERASAKI PLATES. DROPS FORMED FROM A 1:1 MIXTURE OF PROTEIN/DNA COMPLEX (10MG/ML COMPLEX, 20MM TRIS PH 7.5, 1MM EDTA, 0.1M NACL, 15% GLYCEROL) AND 1.4M NACITRATE, 0.1M TRIS PH 7.5., under oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 0.9366 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9366 Å / Relative weight: 1
ReflectionResolution: 2.38→70.67 Å / Num. obs: 95144 / % possible obs: 99.4 % / Redundancy: 2.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.063 / Rrim(I) all: 0.099 / Net I/σ(I): 9.1
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4378 / CC1/2: 0.617 / Rpim(I) all: 0.456 / Rrim(I) all: 0.688 / % possible all: 92.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
MOSFLM7.1.0data reduction
Aimless0.2.17data scaling
PHENIX1.8.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bvs

1bvs
PDB Unreleased entry


Resolution: 2.378→53.06 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.271 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.263 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 4597 -RANDOM
Rwork0.2271 ---
obs0.2282 95116 99.4 %-
Displacement parametersBiso mean: 55.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.9669 Å20 Å20 Å2
2---0.9669 Å20 Å2
3---1.9339 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.378→53.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10228 1220 2 456 11906
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811701HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9516146HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3755SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it11701HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1624SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9777SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion19.43
LS refinement shellResolution: 2.38→2.4 Å
RfactorNum. reflection% reflection
Rfree0.2744 96 -
Rwork0.3042 --
obs0.3027 1903 90.69 %

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