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Open data
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Basic information
Entry | Database: PDB / ID: 1bn5 | ||||||
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Title | HUMAN METHIONINE AMINOPEPTIDASE 2 | ||||||
![]() | METHIONINE AMINOPEPTIDASE | ||||||
![]() | AMINOPEPTIDASE / METHIONINE AMINOPEPTIDASE / HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, S. / Widom, J. / Kemp, C.W. / Crews, C.M. / Clardy, J.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.3 KB | Display | ![]() |
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PDB format | ![]() | 65.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.9 KB | Display | ![]() |
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Full document | ![]() | 381.7 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b59C ![]() 1b6aC ![]() 1boaC ![]() 1xgsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 T-BUTANOL AND COBALT / Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
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→26.5 Å / Num. obs: 42299 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 14.7 |
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: 154879 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XGS Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.12 / Details: BULK SOLVENT CORRECTION FROM X-PLOR USED.
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Displacement parameters | Biso mean: 21.5 Å2
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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 Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |