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Yorodumi- PDB-3b2x: Crystal Structure of E. coli Aminopeptidase N in complex with Lysine -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b2x | ||||||
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Title | Crystal Structure of E. coli Aminopeptidase N in complex with Lysine | ||||||
Components | Aminopeptidase N | ||||||
Keywords | HYDROLASE / Aminopeptidase N / protease / thermolysin / lysin / 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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Addlagatta, A. / Gay, L. / Matthews, B.W. | ||||||
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 | 3b2x.cif.gz | 419.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b2x.ent.gz | 339.3 KB | Display | PDB format |
PDBx/mmJSON format | 3b2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b2x_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
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Full document | 3b2x_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 3b2x_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 3b2x_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/3b2x ftp://data.pdbj.org/pub/pdb/validation_reports/b2/3b2x | HTTPS FTP |
-Related structure data
Related structure data | 3b2pC 3b34C 3b37C 3b3bC 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 (E. coli) / Strain: E. coli K12 / 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, 1232 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-LYS / | #5: Chemical | #6: Chemical | ChemComp-GOL / #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: 3.52 Å3/Da / Density % sol: 65.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0 M 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: Jan 25, 2007 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 201760 / % possible obs: 88.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.092 / Χ2: 1.037 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.532 / Num. unique all: 10919 / Χ2: 0.884 / % possible all: 48.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HPO Resolution: 1.5→49.94 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.088 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.055 / 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: 17.636 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→49.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.541 Å / Total num. of bins used: 20
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