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Yorodumi- PDB-6xuj: HumRadA1 in complex with 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xuj | ||||||
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Title | HumRadA1 in complex with 5-Ethyl-N-(1H-indol-5-ylmethyl)-1,3,4-thiadiazol-2-amine in P21212 | ||||||
Components | DNA repair and recombination protein RadA | ||||||
Keywords | RECOMBINATION / recombinase / ATPase / protein-fragment complex | ||||||
Function / homology | Function and homology information DNA recombinase assembly / mitotic recombination / DNA strand invasion / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Marsh, M.E. / Scott, D.E. / Hyvonen, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To be published Title: Optimising crystallographic systems for structure-guided drug discovery Authors: Brear, P.B. / Marsh, M. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xuj.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xuj.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xuj_validation.pdf.gz | 733.2 KB | Display | wwPDB validaton report |
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Full document | 6xuj_full_validation.pdf.gz | 737.8 KB | Display | |
Data in XML | 6xuj_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6xuj_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/6xuj ftp://data.pdbj.org/pub/pdb/validation_reports/xu/6xuj | HTTPS FTP |
-Related structure data
Related structure data | 6xufC 6yyfC 6yygC 6yykC 4b3bS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25502.150 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O74036 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-O1E / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 50 mM Na/K Phosphate, 5% PEG1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→40.793 Å / Num. obs: 31313 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.929 % / Biso Wilson estimate: 21.363 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.082 / Χ2: 0.937 / Net I/σ(I): 13.77 / Num. measured all: 154352 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4b3b Resolution: 1.54→36.605 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.14 Å2 / Biso mean: 19.1575 Å2 / Biso min: 7.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.54→36.605 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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