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Yorodumi- PDB-3ror: Crystal structure of C105S mutant of Mycobacterium tuberculosis m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ror | ||||||
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Title | Crystal structure of C105S mutant of Mycobacterium tuberculosis methionine aminopeptidase | ||||||
Components | Methionine aminopeptidase | ||||||
Keywords | HYDROLASE / pitabread fold / Methionine excision | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Reddi, R. / Kishor, C. / Addlagatta, A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of C105S mutant of Mycobacterium tuberculosis methionine aminopeptidase Authors: Reddi, R. / Kishor, C. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ror.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ror.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ror.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ror_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 3ror_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 3ror_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3ror_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/3ror ftp://data.pdbj.org/pub/pdb/validation_reports/ro/3ror | HTTPS FTP |
-Related structure data
Related structure data | 1y1nS 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: 31734.717 Da / Num. of mol.: 1 / Mutation: C105S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: map, mapB, MetAP, MT2929, MTV003.07c, Rv2861c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): K12 References: UniProt: P0A5J2, UniProt: P9WK19*PLUS, methionyl aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-BME / | #5: 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: 2.09 Å3/Da / Density % sol: 41.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 2000, Bistris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2004 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.5 Å / Num. all: 15726 / Num. obs: 15726 / % possible obs: 87.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.127 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2364 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y1N Resolution: 2→28.52 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.204 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R Free: 0.225 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.573 Å2
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Refinement step | Cycle: LAST / Resolution: 2→28.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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