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Open data
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Basic information
Entry | Database: PDB / ID: 2bhc | ||||||
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Title | Na substituted E. coli Aminopeptidase P | ||||||
![]() | XAA-PRO AMINOPEPTIDASE | ||||||
![]() | HYDROLASE / PROLINE-SPECIFIC PEPTIDASE / METALLOENZYME / PITA-BREAD FOLD / DINUCLEAR HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M. | ||||||
![]() | ![]() Title: Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, a Metalloprotease with a Dinuclear Metal Center. Authors: Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M. #1: ![]() Title: An Orthorhombic Form of Escherichia Coli Aminopeptidase P at 2.4 Ang Resolution Authors: Graham, S.C. / Lee, M. / Freeman, H.C. / Guss, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.5 KB | Display | ![]() |
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PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.6 KB | Display | ![]() |
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Full document | ![]() | 434.3 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w2mC ![]() 1w7vC ![]() 1wbqC ![]() 1wl6C ![]() 1wl9C ![]() 1wlrC ![]() 2bh3C ![]() 2bhaC ![]() 2bhbC ![]() 2bhdC ![]() 2bn7C ![]() 1n51S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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
#1: Protein | Mass: 49744.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-FLC / |
#5: Water | ChemComp-HOH / |
Compound details | HAS A CATALYTIC ACTIVITY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 77.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN USING HANGING DROP VAPOR DIFFUSION AT 4C. RESERVOIR CONTAINED 26% MPD, 100 MM NA.CITRATE (PH 7.5) AND 200 MM MG.ACETATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 2004 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→60 Å / Num. obs: 43830 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 53.01 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS Resolution: 2.4→60.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SUFFICIENT DENSITY WAS NOT PRESENT TO ALLOW FOR COMPLETE MODELLING OF RESIDUES A439 OR A440
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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: 44.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→60.19 Å
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Refine LS restraints |
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