+Open data
-Basic information
Entry | Database: PDB / ID: 4b3d | ||||||
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Title | Humanised monomeric RadA in complex with 5-methyl indole | ||||||
Components | DNA REPAIR AND RECOMBINATION PROTEIN RADA | ||||||
Keywords | HYDROLASE / RECOMBINASE / THERMOSTABLE / PEPTIDE-BINDING | ||||||
Function / homology | Function and homology information ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | PYROCOCCUS FURIOSUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å | ||||||
Authors | Scott, D.E. / Ehebauer, M.T. / Pukala, T. / Marsh, M. / Blundell, T.L. / Venkitaraman, A.R. / Abell, C. / Hyvonen, M. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: Using a Fragment-Based Approach to Target Protein-Protein Interactions. Authors: Scott, D.E. / Ehebauer, M.T. / Pukala, T. / Marsh, M. / Blundell, T.L. / Venkitaraman, A.R. / Abell, C. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b3d.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b3d.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 4b3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b3d_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 4b3d_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | 4b3d_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 4b3d_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b3d ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b3d | HTTPS FTP |
-Related structure data
Related structure data | 4b2iC 4b2lC 4b32C 4b33C 4b34C 4b35C 4b3bC 4b3cC 1pznS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99993, -0.01187, 0.00085), Vector: |
-Components
#1: Protein | Mass: 25502.150 Da / Num. of mol.: 2 / Fragment: ATPASE / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CONTAINING PUBS520 PLASMID / References: UniProt: O74036 #2: Chemical | #3: Chemical | ChemComp-5MI / #4: 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: 1.83 Å3/Da / Density % sol: 32.37 % / Description: NONE |
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Crystal grow | pH: 6.2 / Details: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→43.62 Å / Num. obs: 57763 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.76 |
Reflection shell | Resolution: 1.59→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.19 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PZN CHAIN A Resolution: 1.589→40.266 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 21.04 / 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 / Bsol: 51.177 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.589→40.266 Å
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Refine LS restraints |
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LS refinement shell |
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