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Yorodumi- PDB-2bn7: Mn substituted E. coli Aminopeptidase P in complex with product and Zn -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bn7 | ||||||
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Title | Mn substituted E. coli Aminopeptidase P in complex with product and Zn | ||||||
Components | XAA-PRO AMINOPEPTIDASE | ||||||
Keywords | HYDROLASE / PROLINE-SPECIFIC PEPTIDASE / PRODUCT COMPLEX / METALLOENZYME / PITA-BREAD FOLD / DINUCLEAR HYDROLASE | ||||||
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: 2.4 Å | ||||||
Authors | Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M. | ||||||
Citation | Journal: Biochemistry / Year: 2005 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bn7.cif.gz | 108.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bn7.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bn7 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bn7 | HTTPS FTP |
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-Related structure data
Related structure data | 1w2mC 1w7vC 1wbqC 1wl6C 1wl9C 1wlrC 2bh3C 2bhaC 2bhbC 2bhcC 2bhdC 1n51S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49744.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DIPEPTIDE PRODUCT OF AMINOPEPTIDASE P (FORMED BY CLEVAGE OF XAA-PRO-LEU TRIPEPTIDE SUBSTRATE) Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: AN1459 / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase |
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-Non-polymers , 7 types, 293 molecules
#2: Chemical | ChemComp-PRO / | ||||||||
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#3: Chemical | ChemComp-LEU / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-FLC / | #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.25 Å3/Da / Density % sol: 76.4 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN IN 22% MPD, 100 MM NACITRATE (PH 7.5) AND 200 MM MGACETATE AT 4C. CRYSTALS WERE SOAKED FOR 1 HOUR IN ...Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN IN 22% MPD, 100 MM NACITRATE (PH 7.5) AND 200 MM MGACETATE AT 4C. CRYSTALS WERE SOAKED FOR 1 HOUR IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2, 1 MM ZNCL2 AND 10 MM PROLEU DIPEPTIDE PRIOR TO DATA COLLECTION. |
-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: Mar 18, 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: 2.4→60 Å / Num. obs: 44853 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 55.06 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS Resolution: 2.4→119.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.752 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSUFFICIENT DENSITY WAS PRESENT TO ALLOW COMPLETE MODELLING OF C-TERMINAL 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: 48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→119.52 Å
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Refine LS restraints |
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