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Yorodumi- PDB-5yr5: Human methionine aminopeptidase type 1b (F309L mutant) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yr5 | ||||||
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Title | Human methionine aminopeptidase type 1b (F309L mutant) in complex with Ovalicin | ||||||
Components | Methionine aminopeptidase 1Methionyl aminopeptidase | ||||||
Keywords | HYDROLASE / Metal binding protein / Methionine Aminopeptidase | ||||||
Function / homology | Function and homology information N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade ...N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / proteolysis / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Pillalamarri, V. / Arya, T. / Addlagatta, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Biochem. J. / Year: 2019 Title: Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis. Authors: Pillalamarri, V. / Arya, T. / Haque, N. / Bala, S.C. / Marapaka, A.K. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yr5.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yr5.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 5yr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/5yr5 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yr5 | HTTPS FTP |
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-Related structure data
Related structure data | 5ykpC 5yr4C 5yr6C 2gz5S C: citing same article (ref.) 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: 34144.891 Da / Num. of mol.: 1 / Fragment: UNP residues 81-384 / Mutation: F309L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53582, methionyl aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-OVA / | #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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1M Bistris pH-6.2, 19% PEG3350, 5% 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: Mar 19, 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: 1.6→50 Å / Num. obs: 45241 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.034 / Rrim(I) all: 0.065 / Χ2: 1.016 / Net I/σ(I): 17.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.417
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GZ5 Resolution: 1.6→31.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.712 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0833 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082 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: 82.85 Å2 / Biso mean: 25.987 Å2 / Biso min: 14.11 Å2
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Refinement step | Cycle: final / Resolution: 1.6→31.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.597→1.638 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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