+Open data
-Basic information
Entry | Database: PDB / ID: 4ook | ||||||
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Title | Third Metal bound M.tuberculosis methionine aminopeptidase | ||||||
Components | Methionine aminopeptidase 2Methionyl aminopeptidase | ||||||
Keywords | HYDROLASE / Aminopeptidases | ||||||
Function / homology | Function and homology information : / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / cobalt ion binding / metalloaminopeptidase activity / protein processing / iron ion binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Reddi, R. / Addlagatta, A. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Selective targeting of the conserved active site cysteine of Mycobacterium tuberculosis methionine aminopeptidase with electrophilic reagents Authors: Reddi, R. / Arya, T. / Kishor, C. / Gumpena, R. / Ganji, R.J. / Bhukya, S. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ook.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ook.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ook.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/4ook ftp://data.pdbj.org/pub/pdb/validation_reports/oo/4ook | HTTPS FTP |
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-Related 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: 30889.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: map, mapB, Rv2861c, MT2929, MTV003.07c / Production host: Escherichia coli (E. coli) References: UniProt: P0A5J2, UniProt: P9WK19*PLUS, methionyl aminopeptidase | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.15 Å3/Da / Density % sol: 42.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 27% PEG 2000, BisTris, Oxidized beta-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.81 Å / Num. obs: 20897 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.437 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.158 / ESU R Free: 0.152 / 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: 29.822 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.81 Å
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