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Yorodumi- PDB-3b3b: Crystal structure of E. coli Aminopeptidase N in complex with try... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b3b | ||||||
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Title | Crystal structure of E. coli Aminopeptidase N in complex with tryptophan | ||||||
Components | Aminopeptidase NAlanine aminopeptidase | ||||||
Keywords | HYDROLASE / Aminopeptidase N / protease / thermolysin / trptophan / Membrane / Metal-binding / Metalloprotease | ||||||
Function / homology | Function and homology information membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Addlagatta, A. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural basis for the unusual specificity of Escherichia coli aminopeptidase N. Authors: Addlagatta, A. / Gay, L. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b3b.cif.gz | 215.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b3b.ent.gz | 167.7 KB | Display | PDB format |
PDBx/mmJSON format | 3b3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/3b3b ftp://data.pdbj.org/pub/pdb/validation_reports/b3/3b3b | HTTPS FTP |
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-Related structure data
Related structure data | 3b2pC 3b2xC 3b34C 3b37C 2hpoS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 101441.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: Aminopeptidase N / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04825, membrane alanyl aminopeptidase |
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-Non-polymers , 6 types, 1012 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-TRP / | #5: Chemical | ChemComp-MLI / | #6: Chemical | #7: 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: 3.53 Å3/Da / Density % sol: 65.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M Sodium Malonate, pH=7.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2007 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 122655 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.054 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 12151 / Rsym value: 0.39 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2HPO Resolution: 1.85→49.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.782 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 17.431 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→49.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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