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Yorodumi- PDB-3b34: Crystal structure of E. coli Aminopeptidase N in complex with Phe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b34 | ||||||
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Title | Crystal structure of E. coli Aminopeptidase N in complex with Phenylalanine | ||||||
Components | Aminopeptidase N | ||||||
Keywords | HYDROLASE / Aminopeptidase N / protease / thermolysin / phenylalanine / 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 / Resolution: 1.3 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 | 3b34.cif.gz | 417.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b34.ent.gz | 338.2 KB | Display | PDB format |
PDBx/mmJSON format | 3b34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b34_validation.pdf.gz | 460.1 KB | Display | wwPDB validaton report |
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Full document | 3b34_full_validation.pdf.gz | 468.7 KB | Display | |
Data in XML | 3b34_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 3b34_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/3b34 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/3b34 | HTTPS FTP |
-Related structure data
Related structure data | 3b2pC 3b2xC 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 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, 1127 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-PHE / | #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: 3.53 Å3/Da / Density % sol: 65.18 % |
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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: Jan 25, 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: 1.3→50 Å / Num. obs: 346171 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.123 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.18 / Num. unique all: 15484 / Rsym value: 0.49 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Starting model: 2HPO Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.973 / SU B: 1.486 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / 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: 18.757 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.335 Å / Total num. of bins used: 20
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