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Open data
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Basic information
Entry | Database: PDB / ID: 2bww | ||||||
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Title | His350Ala Escherichia coli Aminopeptidase P | ||||||
![]() | AMINOPEPTIDASE P | ||||||
![]() | HYDROLASE / AMINOPEPTIDASE P / METALLOENZYME / 'PITA-BREAD' ENZYME / PROLINE-SPECIFIC ENZYME / MANGANESE ENZYME | ||||||
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. / Guss, J.M. | ||||||
![]() | ![]() Title: Kinetic and Crystallographic Analysis of Mutant Escherichia Coli Aminopeptidase P: Insights Into Substrate Recognition and the Mechanism of Catalysis. Authors: Graham, S.C. / Lilley, P.E. / Lee, M. / Schaeffer, P.M. / Kralicek, A.V. / Dixon, N.E. / 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 | ![]() | 105 KB | Display | ![]() |
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PDB format | ![]() | 79.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
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Full document | ![]() | 455.4 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bwsC ![]() 2bwtC ![]() 2bwuC ![]() 2bwvC ![]() 2bwxC ![]() 2bwyC ![]() 2bhcS 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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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: 49676.996 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 157 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-FLC / | #5: Chemical | ChemComp-MRD / ( | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 77.7 % / Description: STARTING MODEL WAS STRIPPED OF HETATMS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 7 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM ...Details: SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 7 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2 FOR 30 MIN AT 4C PRIOR TO CRYOCOOLING. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2005 / 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: 2.6→74.54 Å / Num. obs: 33663 / % possible obs: 97.2 % / Observed criterion σ(I): 6 / Redundancy: 5.4 % / Biso Wilson estimate: 58.02 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 86.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BHC Resolution: 2.61→69.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.361 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PEPTIDE BOND BETWEEN RESIDUES 88 AND 89 IS COMPLETELY DISORDERED AND COULD NOT BE MODELLED. INSUFFICIENT DENSITY WAS PRESENT FOR COMPLETE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PEPTIDE BOND BETWEEN RESIDUES 88 AND 89 IS COMPLETELY DISORDERED AND COULD NOT BE MODELLED. INSUFFICIENT DENSITY WAS PRESENT FOR COMPLETE MODELLING OF RESIDUES 439 AND 440
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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: 44.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→69.67 Å
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Refine LS restraints |
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