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- PDB-4pqy: Mycobacterium tuberculosis RecA glycerol bound low temperature st... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pqy | ||||||
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Title | Mycobacterium tuberculosis RecA glycerol bound low temperature structure IIC-N4 | ||||||
![]() | Protein RecA, 1st part, 2nd part | ||||||
![]() | HYDROLASE / HOMOLOGOUS RECOMBINATION / DNA REPAIR / ATPASE / RECOMBINASE / DNA BINDING PROTEIN / PLOOP CONTAINING NTPASE FOLD / ATP BINDING / HYDROLYSIS | ||||||
Function / homology | ![]() UV protection / DNA strand invasion / intein-mediated protein splicing / intron homing / DNA strand exchange activity / recombinational repair / ATP-dependent DNA damage sensor activity / SOS response / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...UV protection / DNA strand invasion / intein-mediated protein splicing / intron homing / DNA strand exchange activity / recombinational repair / ATP-dependent DNA damage sensor activity / SOS response / ATP-dependent activity, acting on DNA / DNA endonuclease activity / manganese ion binding / single-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / response to antibiotic / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chandran, A.V. / Prabu, J.R. / Patil, N.K. / Muniyappa, K. / Vijayan, M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 53.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4oqfC ![]() 4po1C ![]() 4po8C ![]() 4po9C ![]() 4poaC ![]() 4ppfC ![]() 4ppgC ![]() 4ppnC ![]() 4ppqC ![]() 4pqfC ![]() 4pqrC ![]() 4pr0C ![]() 4psaC ![]() 4pskC ![]() 4psvC ![]() 4ptlC ![]() 1g19S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-GOL / |
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 15% PEG 3350, 10% PEG 5000 MME, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 12, 2012 / Details: MIRRORS |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→70.69 Å / Num. obs: 9884 / Redundancy: 4 % / Biso Wilson estimate: 67.7 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1429 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G19 Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.814 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / 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: 42.224 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / Total num. of bins used: 20
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