+Open data
-Basic information
Entry | Database: PDB / ID: 2bws | ||||||
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Title | His243Ala Escherichia coli Aminopeptidase P | ||||||
Components | XAA-PRO AMINOPEPTIDASE P | ||||||
Keywords | HYDROLASE / METALLOENZYME / 'PITA-BREAD' ENZYME / PROLINE-SPECIFIC ENZYME / MANGANESE ENZYME | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Graham, S.C. / Guss, J.M. | ||||||
Citation | Journal: Biochemistry / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bws.cif.gz | 117.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bws.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/2bws ftp://data.pdbj.org/pub/pdb/validation_reports/bw/2bws | HTTPS FTP |
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-Related structure data
Related structure data | 2bwtC 2bwuC 2bwvC 2bwwC 2bwxC 2bwyC 1wl9S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 49692.992 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: AN1459 / Plasmid: PPL670/H243A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 71.8 % Description: STARTING MODEL WAS STRIPPED OF HETATMS AND MULTIPLE CONFORMERS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 6 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28 % PEG 4K, 0.1 M TRIS PH 8.2. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 ...Details: HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 6 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28 % PEG 4K, 0.1 M TRIS PH 8.2. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD 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: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 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: 1.75→76.7 Å / Num. obs: 86631 / % possible obs: 97.3 % / Observed criterion σ(I): 6 / Redundancy: 5 % / Biso Wilson estimate: 21.28 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.4 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WL9 Resolution: 1.75→60.08 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.204 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→60.08 Å
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Refine LS restraints |
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