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Yorodumi- PDB-2b3h: Crystal structure of Human Methionine Aminopeptidase Type I with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b3h | ||||||
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Title | Crystal structure of Human Methionine Aminopeptidase Type I with a third cobalt in the active site | ||||||
Components | Methionine aminopeptidase 1 | ||||||
Keywords | HYDROLASE / methionine aminopeptidase / metalloprotease / pitabread fold | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Addlagatta, A. / Hu, X. / Liu, J.O. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural Basis for the Functional Differences between Type I and Type II Human Methionine Aminopeptidases(,). Authors: Addlagatta, A. / Hu, X. / Liu, J.O. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b3h.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b3h.ent.gz | 125.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b3h_validation.pdf.gz | 415 KB | Display | wwPDB validaton report |
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Full document | 2b3h_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 2b3h_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2b3h_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/2b3h ftp://data.pdbj.org/pub/pdb/validation_reports/b3/2b3h | HTTPS FTP |
-Related structure data
Related structure data | 2b3kC 2b3lC 1yj3S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36935.926 Da / Num. of mol.: 1 / Fragment: residues 81-384 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1, KIAA0094 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53582, methionyl aminopeptidase |
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-Non-polymers , 5 types, 519 molecules
#2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2000, potassium chloride, hepes, sodium chloride, pH 6.5, 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: 0.977 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2005 / Details: mirror |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. all: 142947 / Num. obs: 142947 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.045 / Χ2: 1.002 / Net I/σ(I): 60.37 |
Reflection shell | Resolution: 1.1→1.12 Å / % possible obs: 72.7 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 4.7 / Num. measured obs: 9989 / Χ2: 1.081 / % possible all: 78.9 |
-Phasing
Phasing MR | Rfactor: 0.576 / Cor.coef. Fo:Fc: 0.678
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1YJ3 Resolution: 1.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.703 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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