[English] 日本語
Yorodumi- PDB-5yoh: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yoh | ||||||
---|---|---|---|---|---|---|---|
Title | Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105M mutant) in complex with Methionine | ||||||
Components | Methionine aminopeptidaseMethionyl aminopeptidase | ||||||
Keywords | HYDROLASE / Methionine aminopeptidase | ||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Ra (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å | ||||||
Authors | Sandeep, C.B. / Addlagatta, A. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: To Be Published Title: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105M mutant) in complex with Methionine Authors: Sandeep, C.B. / Addlagatta, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yoh.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yoh.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/5yoh ftp://data.pdbj.org/pub/pdb/validation_reports/yo/5yoh | HTTPS FTP |
---|
-Related structure data
Related structure data | 1yj3S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34470.824 Da / Num. of mol.: 1 / Mutation: C105M, C284A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria) Strain: H37Ra / Gene: mapB, map, MRA_2886 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U6L5, methionyl aminopeptidase |
---|
-Non-polymers , 5 types, 211 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-MET / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.86 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 27% Peg3350, 3% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 25, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→28.59 Å / Num. obs: 32311 / % possible obs: 92.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.026 / Rrim(I) all: 0.038 / Χ2: 1.028 / Net I/av σ(I): 18.94 / Net I/σ(I): 59.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 1.9 %
|
-Phasing
Phasing | Method: molecular replacement | ||||||
---|---|---|---|---|---|---|---|
Phasing MR | R rigid body: 0.38
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YJ3 Resolution: 1.63→28.59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.552 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.102 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.9 Å2 / Biso mean: 23.683 Å2 / Biso min: 11.41 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.63→28.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.625→1.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|