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Yorodumi- PDB-1kq9: Human methionine aminopeptidase type II in complex with L-methionine -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kq9 | ||||||
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Title | Human methionine aminopeptidase type II in complex with L-methionine | ||||||
Components | Methionine aminopeptidase 2 | ||||||
Keywords | HYDROLASE / central b-sheet and two pairs of a-helices | ||||||
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 / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding ...N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Nonato, M.C. / Widom, J. / Clardy, J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Human methionine aminopeptidase type 2 in complex with L- and D-methionine Authors: Nonato, M.C. / Widom, J. / Clardy, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kq9.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kq9.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kq9_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 1kq9_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 1kq9_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1kq9_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/1kq9 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/1kq9 | HTTPS FTP |
-Related structure data
Related structure data | 1kq0C 1bn5S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 52985.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MET / | #4: Chemical | ChemComp-TBU / | #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: 2.73 Å3/Da / Density % sol: 42.09 % / Description: 54.6 | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 18-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT (DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: bent conical Si-mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→66 Å / Num. obs: 33600 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 3.24 % / Biso Wilson estimate: 21.07 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 23.24 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.046 / Num. unique all: 3411 / % possible all: 96.5 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % possible obs: 94 % / Redundancy: 3.4 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1BN5 Resolution: 1.9→66 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.303 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→66 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.181 | ||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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