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Yorodumi- PDB-5yxf: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C10... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yxf | ||||||
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Title | Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105L mutant) in complex with Methionine | ||||||
Components | Methionine aminopeptidase | ||||||
Keywords | HYDROLASE / Methionine aminopeptidase | ||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / transition metal ion binding / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å | ||||||
Authors | Sandeep, C.B. / Addlagatta, A. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105L mutant) in complex with Methionine Authors: Sandeep, C.B. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yxf.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yxf.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yxf_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 5yxf_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 5yxf_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5yxf_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/5yxf ftp://data.pdbj.org/pub/pdb/validation_reports/yx/5yxf | HTTPS FTP |
-Related structure data
Related structure data | 1yj3S 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: 34452.785 Da / Num. of mol.: 1 / Mutation: C105L, C284A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria) Strain: ATCC 25177 / H37Ra / Gene: mapB, map, MRA_2886 / Production host: Escherichia coli (E. coli) / References: UniProt: A5U6L5, methionyl aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-MET / | #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: 1.94 Å3/Da / Density % sol: 36.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes pH 7.5, 27% Peg3350, 3% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→35.37 Å / Num. obs: 33848 / % possible obs: 96.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.75 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.052 / Rrim(I) all: 0.076 / Χ2: 1.043 / Net I/av σ(I): 11.66 / Net I/σ(I): 17.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.383
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YJ3 Resolution: 1.61→35.37 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.133 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0898 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.18 Å2 / Biso mean: 31.845 Å2 / Biso min: 16.9 Å2
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Refinement step | Cycle: final / Resolution: 1.61→35.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.608→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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