+Open data
-Basic information
Entry | Database: PDB / ID: 2bhd | ||||||
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Title | Mg substituted E. coli Aminopeptidase P in complex with product | ||||||
Components |
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Keywords | HYDROLASE / HYDROLASE-SUBSTRATE COMPLEX / PROLINE-SPECIFIC PEPTIDASE / PRODUCT COMPLEX / METALLOENZYME / PITA-BREAD FOLD / DINUCLEAR HYDROLASE / AMINOPEPTIDASE / MANGANESE / METAL-BINDING / METALLOPROTEASE | ||||||
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) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 2bhd.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bhd.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/2bhd ftp://data.pdbj.org/pub/pdb/validation_reports/bh/2bhd | HTTPS FTP |
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-Related structure data
Related structure data | 1w2mC 1w7vC 1wbqC 1wl6C 1wl9C 1wlrC 2bh3C 2bhaC 2bhbC 2bhcC 2bn7C 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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Details | AMINOPEPTIDASE P IS A HOMOTETRAMER IN SOLUTION. HOWEVER, SINCE IN THIS ENTRY, EACH CHAIN OF THIS PROTEIN IS IN COMPLEX WITH A TRIPEPTIDE, THIS ENTRY IS CLASSIFIED AS A HETEROOCTAMER. |
-Components
#1: Protein | Mass: 49744.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Variant: AN1459 / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase | ||||
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#2: Protein/peptide | Mass: 327.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TRIPEPTIDE SUBSTRATE OF AMINOPEPTIDASE P / Source: (synth.) SYNTHETIC CONSTRUCT (others) | ||||
#3: Chemical | #4: Chemical | ChemComp-FLC / | #5: 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: 5.6 Å3/Da / Density % sol: 77.8 % |
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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 VAOPR DIFFUSION AT 4C. RESERVOIR CONTAINED 26% MPD, 100 MM NA.CITRATE (PH 7.5) AND ...Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN USING HANGING DROP VAOPR DIFFUSION AT 4C. RESERVOIR CONTAINED 26% MPD, 100 MM NA.CITRATE (PH 7.5) AND 200 MM MG.ACETATE. CRYSTALS WERE SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10 MM VALPROLEU TRIPEPTIDE FOR 20 HOURS AT 4C 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: 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: 2.5→60 Å / Num. obs: 38892 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 55.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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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: 2.5→60.19 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SUFFICIENT DENSITY WAS NOT PRESENT TO ALLOW FULL MODELLING OF RESIDUES A439 AND A440. A PROLEU DIPEPTIDE IS VISIBLE IN THE ACTIVE SITE. IT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SUFFICIENT DENSITY WAS NOT PRESENT TO ALLOW FULL MODELLING OF RESIDUES A439 AND A440. A PROLEU DIPEPTIDE IS VISIBLE IN THE ACTIVE SITE. IT IS ASSUMED THAT CONTAMINATING ACTIVITY IN THE DROP CLEAVED ALL OF THE VALPROLEU PEPTIDE PRESENT IN THE DROP, LEAVING ONLY PROLEU WHICH BINDS TO THE ENZYME AS A PRODUCT INHIBITOR.
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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: 43.16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→60.19 Å
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Refine LS restraints |
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