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Yorodumi- PDB-1boa: HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH ANGIOGENESIS INH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1boa | ||||||
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Title | HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH ANGIOGENESIS INHIBITOR FUMAGILLIN | ||||||
Components | METHIONINE AMINOPEPTIDASE | ||||||
Keywords | AMINOPEPTIDASE / METHIONINE AMINOPEPTIDASE / ANGIOGENESIS INHIBITOR / FUMAGILLIN / HYDROLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, S. / Widom, J. / Kemp, C.W. / Crews, C.M. / Clardy, J.C. | ||||||
Citation | Journal: Science / Year: 1998 Title: Structure of human methionine aminopeptidase-2 complexed with fumagillin. Authors: Liu, S. / Widom, J. / Kemp, C.W. / Crews, C.M. / Clardy, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1boa.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1boa.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 1boa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1boa_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 1boa_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 1boa_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1boa_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/1boa ftp://data.pdbj.org/pub/pdb/validation_reports/bo/1boa | HTTPS FTP |
-Related structure data
Related structure data | 1b59C 1b6aC 1bn5C 1xgsS S: Starting model for refinement C: citing same article (ref.) |
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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: 52985.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH FUMAGILLIN AND COBALT / Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Cell line (production host): SF21 CELLS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-FUG / | #4: 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: 2.8 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.4 / Details: pH 5.4 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 1998 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.922 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→26.6 Å / Num. obs: 40944 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 6.8 / Rsym value: 0.149 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 158945 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XGS Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.12 / Details: BULK SOLVENT CORRECTION FROM X-PLOR USED.
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Displacement parameters | Biso mean: 23.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Rfactor obs: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |