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Yorodumi- PDB-3fmq: Crystal structure of an Encephalitozoon cuniculi methionine amino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fmq | |||||||||
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Title | Crystal structure of an Encephalitozoon cuniculi methionine aminopeptidase type 2 with angiogenesis inhibitor fumagillin bound | |||||||||
Components | Methionine aminopeptidase 2Methionyl aminopeptidase | |||||||||
Keywords | HYDROLASE / METHIONINE AMINOPEPTIDASE TYPE2 / METAP2 / METAP2 FUMAGILLIN COMPLEX / ENCEPHALITOZOON CUNICULI / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / Aminopeptidase / Cobalt / Metal-binding / Protease | |||||||||
Function / homology | Function and homology information initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / proteolysis / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Encephalitozoon cuniculi (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å | |||||||||
Authors | Alvarado, J.J. / Russell, M. / Zhang, A. / Adams, J. / Toro, R. / Burley, S.K. / Weiss, L.M. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | |||||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2009 Title: Structure of a microsporidian methionine aminopeptidase type 2 complexed with fumagillin and TNP-470. Authors: Alvarado, J.J. / Nemkal, A. / Sauder, J.M. / Russell, M. / Akiyoshi, D.E. / Shi, W. / Almo, S.C. / Weiss, L.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fmq.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fmq.ent.gz | 120.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fmq ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fmq | HTTPS FTP |
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-Related structure data
Related structure data | 3fm3SC 3fmrC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40029.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Strain: GB-M1 / Gene: ECU10_0750, MAP2 / Plasmid: pBAC2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8SR45, methionyl aminopeptidase #2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | FUMAGILLIN (FUG) FORMS A COVALENT BOND WITH HISTIDINE 109. IN BOTH FUMAGILLIN MOLECULES THAT ARE ...FUMAGILLIN | |
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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: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 27% PEG 4000, 0.2M Ammonium sulfate, 0.5mM Fumagillin. Cryosolution: 30% PEG 4000, 0.2M Ammonium sulfate, 10% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 25402 / % possible obs: 97.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.126 / Χ2: 0.84 / Net I/σ(I): 9.444 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3FM3 Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.152 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.847 / SU B: 8.98 / SU ML: 0.2 / SU R Cruickshank DPI: 1.181 / SU Rfree: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.18 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.54 Å2 / Biso mean: 18.202 Å2 / Biso min: 2.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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