+Open data
-Basic information
Entry | Database: PDB / ID: 1a16 | ||||||
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Title | AMINOPEPTIDASE P FROM E. COLI WITH THE INHIBITOR PRO-LEU | ||||||
Components | AMINOPEPTIDASE P | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PROLINE PEPTIDASE-DIPEPTIDE INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.3 Å | ||||||
Authors | Wilce, M.C. / Bond, C.S. / Lilley, P.E. / Dixon, N.E. / Freeman, H.C. / Guss, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. Authors: Wilce, M.C. / Bond, C.S. / Dixon, N.E. / Freeman, H.C. / Guss, J.M. / Lilley, P.E. / Wilce, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a16.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a16.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a16_validation.pdf.gz | 399.3 KB | Display | wwPDB validaton report |
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Full document | 1a16_full_validation.pdf.gz | 407.5 KB | Display | |
Data in XML | 1a16_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1a16_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a16 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a16 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49744.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Strain: AN1459/PPL670 / References: UniProt: P15034, Xaa-Pro aminopeptidase | ||||
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#2: Chemical | ChemComp-PRO / | ||||
#3: Chemical | ChemComp-LEU / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR DIPEPTIDE PRO-LEU BINDS IN THE ACTIVE SITE CLOSE TO THE DINUCLEAR MANGANESE CENTER. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.3 Details: pH 8.3 THE CRYSTALS WERE SOAKED IN A SOLUTION CONTAINING PRO-LEU, AN INHIBITOR. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop contained 1:1 mixture of protein and reservoir solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 58976 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 19.2 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 15 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.197 / % possible all: 84.9 |
Reflection | *PLUS Num. obs: 36900 / % possible obs: 91.9 % / Num. measured all: 549017 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 92 % / Rmerge(I) obs: 0.375 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→50 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2513 |