+Open data
-Basic information
Entry | Database: PDB / ID: 1in5 | ||||||
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Title | THERMOGOTA MARITIMA RUVB A156S MUTANT | ||||||
Components | HOLLIDAY JUNCTION DNA HELICASE RUVB | ||||||
Keywords | DNA BINDING PROTEIN / AAA+-Class ATPase / Winged-Helix Domain / Holliday Junction / Branch Migration / 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 | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Putnam, C.D. / Clancy, S.B. / Tsuruta, H. / Gonzalez, S. / Wetmur, J.G. / Tainer, J.A. | ||||||
Citation | Journal: 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 |
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Remark 300 | BIOMOLECULE: 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1in5.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1in5.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 1in5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1in5_validation.pdf.gz | 780.9 KB | Display | wwPDB validaton report |
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Full document | 1in5_full_validation.pdf.gz | 785 KB | Display | |
Data in XML | 1in5_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1in5_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/1in5 ftp://data.pdbj.org/pub/pdb/validation_reports/in/1in5 | HTTPS FTP |
-Related structure data
Related structure data | 1in4SC 1in6C 1in7C 1in8C 1j7kC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 37222.180 Da / Num. of mol.: 1 / Mutation: A156S 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 |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.83 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 23564 / Num. obs: 23654 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2167 / % possible all: 91.4 |
Reflection | *PLUS Num. measured all: 81462 |
Reflection shell | *PLUS % possible obs: 91.4 % / Rmerge(I) obs: 0.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IN4 Resolution: 2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1789482.7 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.99 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.284 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.244 |