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Yorodumi- PDB-4psv: Mycobacterium tuberculosis RecA phosphate bound room temperature ... -
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-Basic information
Entry | Database: PDB / ID: 4psv | ||||||
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Title | Mycobacterium tuberculosis RecA phosphate bound room temperature structure I-RT | ||||||
Components | Protein RecA, 1st part, 2nd part | ||||||
Keywords | HYDROLASE / HOMOLOGOUS RECOMBINATION / DNA REPAIR / ATPASE / RECOMBINASE / DNA BINDING PROTEIN / PLOOP CONTAINING NTPASE FOLD / ATP BINDING / HYDROLYSIS | ||||||
Function / homology | Function and homology information DNA strand invasion / DNA strand exchange activity / UV protection / intron homing / intein-mediated protein splicing / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...DNA strand invasion / DNA strand exchange activity / UV protection / intron homing / intein-mediated protein splicing / recombinational repair / SOS response / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity / single-stranded DNA binding / manganese ion binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / response to antibiotic / DNA repair / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Chandran, A.V. / Prabu, J.R. / Patil, N.K. / Muniyappa, K. / Vijayan, M. | ||||||
Citation | Journal: J.Biosci. / Year: 2015 Title: Structural studies on Mycobacterium tuberculosis RecA: Molecular plasticity and interspecies variability Authors: Chandran, A.V. / Prabu, J.R. / Nautiyal, A. / Patil, K.N. / Muniyappa, K. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes Authors: Prabu, J.R. / Manjunath, G.P. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. #2: Journal: Nucleic Acids Res. / Year: 2006 Title: Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery Authors: Krishna, R. / Manjunath, G.P. / Kumar, P. / Surolia, A. / Chandra, N.R. / Muniyappa, K. / Vijayan, M. #3: 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. #4: 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. #5: Journal: Nucleic Acids Res. / Year: 2000 Title: Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation Authors: Datta, S. / Prabu, M.M. / Vaze, M.B. / 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 | 4psv.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4psv.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 4psv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4psv ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4psv | HTTPS FTP |
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-Related structure data
Related structure data | 4oqfC 4po1C 4po8C 4po9C 4poaC 4ppfC 4ppgC 4ppnC 4ppqC 4pqfC 4pqrC 4pqyC 4pr0C 4psaC 4pskC 4ptlC 1g19S C: citing same article (ref.) S: Starting model for refinement |
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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: 37222.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2806, MTV002.02c, recA, Rv2737c / Plasmid: PEJ135 / Production host: Escherichia coli (E. coli) / Strain (production host): KM4104 References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | THE PROTEIN IS EXPRESSED AS A 790 AMINO ACID RESIDUE PRECURSOR (UNIPROT P0A5U4). ONCE IT IS ...THE PROTEIN IS EXPRESSED AS A 790 AMINO ACID RESIDUE PRECURSOR (UNIPROT P0A5U4). ONCE IT IS RELEASED INTO THE CELL, THE CHAIN MTU RECA INTEIN (RESIDUES 252-691) IS CLEAVED OFF, CHAINS 1ST PART (RESIDUES 1-251) AND 2ND PART (RESIDUES 692-790) JOIN TOGETHER TO FORM THE MATURE PROTEIN. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 30% PEG 3350, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.98 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2007 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 14941 / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.9 |
Reflection shell | Highest resolution: 2.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1489 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G19 Resolution: 2.6→27.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.268 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.242 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→27.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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