+Open data
-Basic information
Entry | Database: PDB / ID: 1ube | ||||||
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Title | MsRecA-ADP Complex | ||||||
Components | RecA | ||||||
Keywords | RECOMBINATION / DNA-REPAIR | ||||||
Function / homology | Function and homology information SOS response / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / DNA recombination / damaged DNA binding / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Datta, S. / Krishna, R. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. | ||||||
Citation | Journal: J.BACTERIOL. / Year: 2003 Title: Crystal Structures of Mycobacterium smegmatis RecA and Its Nucleotide Complexes Authors: Datta, S. / Krishna, R. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. #1: Journal: Nucleic Acids Res. / Year: 2000 Title: Crystal Structures of Mycobacterium Tuberculosis Reca and its Complex with Adp-Alf4: Implications For Decreased ATPase Activity and Molecular Aggregation Authors: Datta, S. / Prabu, M. / Vaze, M.B. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. #2: Journal: Proteins / Year: 2003 Title: Structural studies on MtRecA-nucleotide complexes: Insights into DNA and nucleotide binding and the structural signature of NTP recognition Authors: Datta, S. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ube.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ube.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ube.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/1ube ftp://data.pdbj.org/pub/pdb/validation_reports/ub/1ube | HTTPS FTP |
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-Related structure data
Related structure data | 1ubcC 1ubfC 1ubgC 1g19S 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: 37344.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Plasmid: pThioA / Production host: Escherichia coli (E. coli) / Strain (production host): JC10289 / References: UniProt: Q59560 |
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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: 3.5 Å3/Da / Density % sol: 64.57 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, CIT_PHOS, NACL, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 2002 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. all: 6846 / Num. obs: 6339 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.5 / Num. unique all: 649 / % possible all: 93.8 |
Reflection | *PLUS Highest resolution: 3.3 Å |
Reflection shell | *PLUS Highest resolution: 3.3 Å / % possible obs: 93.8 % / Num. unique obs: 649 / Rmerge(I) obs: 0.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1g19 Resolution: 3.3→15 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 159582.44 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.2327 Å2 / ksol: 0.19912 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.5 Å / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.3 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.228 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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