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Yorodumi- PDB-1b59: COMPLEX OF HUMAN METHIONINE AMINOPEPTIDASE-2 COMPLEXED WITH OVALICIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b59 | ||||||
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Title | COMPLEX OF HUMAN METHIONINE AMINOPEPTIDASE-2 COMPLEXED WITH OVALICIN | ||||||
Components | PROTEIN (METHIONINE AMINOPEPTIDASE) | ||||||
Keywords | HYDROLASE / ANGIOGENESIS INHIBITOR | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, S. / 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 | 1b59.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b59.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/1b59 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/1b59 | HTTPS FTP |
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-Related structure data
Related structure data | 1b6aC 1bn5SC 1boaC 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: 41453.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: OVALICIN COVALENTLY LINKED TO HIS 231 NE2 / Source: (gene. exp.) Homo sapiens (human) Description: PROTEIN WAS EXPRESSED IN SF21 INSECT CELLS.. BACULOVIRUS PACSG2 VECTOR Cellular location: CYTOPLASM / Genus (production host): Nucleopolyhedrovirus / Cell line (production host): SF21 / Production host: Spodoptera frugiperda MNPV (virus) / Strain (production host): SF21 / References: UniProt: P50579, methionyl aminopeptidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-OVA / | #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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | pH: 5.4 / Details: 15-30% T-BUTANOL, 50MM CITRATE BUFFER PH=5.2-5.4 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 |
Detector | Type: ADSC / Detector: CCD / Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. obs: 40120 / % possible obs: 96.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.298 / % possible all: 97.7 |
Reflection | *PLUS Lowest resolution: 25 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BN5 Resolution: 1.8→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2190766.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.762 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.303 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.234 |