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Open data
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Basic information
Entry | Database: PDB / ID: 2bwu | ||||||
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Title | Asp271Ala 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 | ![]() | 104 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.9 KB | Display | ![]() |
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Full document | ![]() | 443.6 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bwsC ![]() 2bwtC ![]() 2bwvC ![]() 2bwwC ![]() 2bwxC ![]() 2bwyC ![]() 2bhcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 49700.055 Da / Num. of mol.: 1 / Mutation: YES 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 | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 77.9 % / 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 10 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 30% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH AND 1 MM ...Details: SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 10 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 30% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH AND 1 MM MNCL2 FOR 1 HR AT 4C PRIOR TO CRYOCOOLING. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 3, 2005 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98086 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→22.58 Å / Num. obs: 56922 / % possible obs: 99.4 % / Observed criterion σ(I): 6 / Redundancy: 4.1 % / Biso Wilson estimate: 50.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BHC Resolution: 2.2→22.65 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 8.096 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSUFFICIENT DENSITY WAS AVAILABLE FOR COMPLETE MODELLING OF RESIDUES 439-440. THE METAL SITE IS HIGHLY DISORDERED AND THE POSSIBILITY OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSUFFICIENT DENSITY WAS AVAILABLE FOR COMPLETE MODELLING OF RESIDUES 439-440. THE METAL SITE IS HIGHLY DISORDERED AND THE POSSIBILITY OF METAL HETEROGENEITY CANNOT BE DISCOUNTED.
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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: 57.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→22.65 Å
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Refine LS restraints |
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