[English] 日本語
![](img/lk-miru.gif)
- PDB-4po1: Mycobacterium tuberculosis RecA glycerol bound room temperature s... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4po1 | ||||||
---|---|---|---|---|---|---|---|
Title | Mycobacterium tuberculosis RecA glycerol bound room temperature structure IIC-RT | ||||||
![]() | Protein RecA | ||||||
![]() | DNA BINDING PROTEIN / HOMOLOGOUS RECOMBINATION / DNA REPAIR / ATPASE / 'P-LOOP CONTAINING NTPASE' FOLD / HYDROLYSIS / ATP BINDING | ||||||
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 / 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 / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 70.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 440.7 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oqfC ![]() 4po8C ![]() 4po9C ![]() 4poaC ![]() 4ppfC ![]() 4ppgC ![]() 4ppnC ![]() 4ppqC ![]() 4pqfC ![]() 4pqrC ![]() 4pqyC ![]() 4pr0C ![]() 4psaC ![]() 4pskC ![]() 4psvC ![]() 4ptlC ![]() 1g19S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37222.238 Da / Num. of mol.: 1 / Fragment: UNP residues 1-252, UNP residues 692-771 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, Hydrolases; Acting on ester bonds |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT ONCE A CHAIN (790 AMINO ACIDS, FULL LENGTH) IS RELEASED INTO THE CELL, THE CHAIN ...AUTHORS STATE THAT ONCE A CHAIN (790 AMINO ACIDS, FULL LENGTH) IS RELEASED INTO THE CELL, THE CHAIN IS CLEAVED OFF AND THE PEPTIDE STRETCHES 1-251 AND 692-790 JOIN TOGETHER TO FORM THE MATURE PROTEIN. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.75 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 15% PEG3350, 10% PEG5000 MME, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 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: 3.4→57.39 Å / Num. obs: 6799 / Redundancy: 6 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.337 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.6 / Num. unique all: 981 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1G19 Resolution: 3.4→21.15 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.875 / SU B: 20.655 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 43.313 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→21.15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.4→3.487 Å / Total num. of bins used: 20
|