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Yorodumi- PDB-4aa2: Crystal structure of ANCE in complex with bradykinin potentiating... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aa2 | |||||||||
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Title | Crystal structure of ANCE in complex with bradykinin potentiating peptide b | |||||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / HYDROLASE / SUBSTRATE BINDING / INHIBITOR | |||||||||
Function / homology | Function and homology information Metabolism of Angiotensinogen to Angiotensins / metamorphosis / response to symbiotic bacterium / peptidyl-dipeptidase A / metalloendopeptidase inhibitor activity / sexual reproduction / peptide hormone processing / peptidyl-dipeptidase activity / carboxypeptidase activity / regulation of blood pressure ...Metabolism of Angiotensinogen to Angiotensins / metamorphosis / response to symbiotic bacterium / peptidyl-dipeptidase A / metalloendopeptidase inhibitor activity / sexual reproduction / peptide hormone processing / peptidyl-dipeptidase activity / carboxypeptidase activity / regulation of blood pressure / vasodilation / hormone activity / metallopeptidase activity / toxin activity / proteolysis / extracellular space / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) GLOYDIUS BLOMHOFFI (mamushi) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | |||||||||
Authors | Isaac, R.E. / Akif, M. / Schwager, S.L.U. / Masuyer, G. / Sturrock, E.D. / Acharya, K.R. | |||||||||
Citation | Journal: FEBS J. / Year: 2012 Title: Structural Basis of Peptide Recognition by the Angiotensin-I Converting Enzyme Homologue Ance from Drosophila Melanogaster Authors: Akif, M. / Masuyer, G. / Bingham, R.J. / Sturrock, E.D. / Isaac, R.E. / Acharya, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aa2.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aa2.ent.gz | 113.3 KB | Display | PDB format |
PDBx/mmJSON format | 4aa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aa2_validation.pdf.gz | 851.9 KB | Display | wwPDB validaton report |
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Full document | 4aa2_full_validation.pdf.gz | 854.1 KB | Display | |
Data in XML | 4aa2_validation.xml.gz | 27 KB | Display | |
Data in CIF | 4aa2_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/4aa2 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/4aa2 | HTTPS FTP |
-Related structure data
Related structure data | 4aa1C 4asqC 4asrC 2x8yS 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
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 69152.602 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-614 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PPIC9 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: Q10714, peptidyl-dipeptidase A |
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#2: Protein/peptide | Mass: 1202.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) GLOYDIUS BLOMHOFFI (mamushi) / References: UniProt: P01021 |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 2 types, 418 molecules
#4: Chemical | ChemComp-ZN / |
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#6: 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: 4.3 Å3/Da / Density % sol: 71 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M HEPES 7.5, 1.3 M SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 78895 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.5 / % possible all: 85.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X8Y Resolution: 1.99→38.1 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.841 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY RESIDUES ARG6 TO PRO11 OF BPPB WERE VISIBLE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.556 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→38.1 Å
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