+Open data
-Basic information
Entry | Database: PDB / ID: 7oa5 | ||||||
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Title | RUVA COMPLEXED TO A HOLLIDAY JUNCTION. | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Complex / DNA Binding | ||||||
Function / homology | Function and homology information Holliday junction helicase complex / four-way junction helicase activity / SOS response / DNA recombination / DNA helicase / hydrolase activity / DNA repair / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Mycobacterium leprae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.378 Å | ||||||
Authors | Roe, S.M. / Pearl, L.H. | ||||||
Citation | Journal: Molecular Cell / Year: 1998 Title: Crystal structure of an octameric RuvA-Holliday junction complex Authors: Roe, S.M. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oa5.cif.gz | 306.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oa5.ent.gz | 243.6 KB | Display | PDB format |
PDBx/mmJSON format | 7oa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/7oa5 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oa5 | HTTPS FTP |
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-Related structure data
Related structure data | 1bvs S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | 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 | Mass: 4600.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria) |
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#3: DNA chain | Mass: 4274.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria) |
#4: DNA chain | Mass: 4899.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria) |
#5: DNA chain | Mass: 4585.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium leprae (bacteria) |
-Non-polymers , 2 types, 458 molecules
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63 % / Description: Trigonal bipyramidal |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 0.9366 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9366 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bvs 1bvs 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
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Displacement parameters | Biso mean: 55.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.378→53.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.4 Å
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