+Open data
-Basic information
Entry | Database: PDB / ID: 1j7k | ||||||
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Title | THERMOTOGA MARITIMA RUVB P216G MUTANT | ||||||
Components | HOLLIDAY JUNCTION DNA HELICASE RUVB | ||||||
Keywords | DNA BINDING PROTEIN / AAA+-Class ATPase / Winged-Helix Domain / DNA Translocase / 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: 1.8 Å | ||||||
Authors | Putnam, C.D. / Clancy, S.B. / Tsuruta, H. / 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 | 1j7k.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j7k.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j7k_validation.pdf.gz | 791 KB | Display | wwPDB validaton report |
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Full document | 1j7k_full_validation.pdf.gz | 793 KB | Display | |
Data in XML | 1j7k_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1j7k_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j7k ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j7k | HTTPS FTP |
-Related structure data
Related structure data | 1in4SC 1in5C 1in6C 1in7C 1in8C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37166.113 Da / Num. of mol.: 1 / Mutation: P216G 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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-Non-polymers , 5 types, 268 molecules
#2: Chemical | #3: Chemical | ChemComp-CO / | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-HEZ / | #6: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.11 % | ||||||||||||||||||||||||
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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: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 29, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 37484 / Num. obs: 37484 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.044 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3602 / % possible all: 94.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 136037 |
Reflection shell | *PLUS % possible obs: 94.8 % / Rmerge(I) obs: 0.332 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IN4 Resolution: 1.8→19.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1830642.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.88 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / 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: 10.1 % / Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.251 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.229 |