+Open data
-Basic information
Entry | Database: PDB / ID: 6bv0 | |||||||||
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Title | Crystal structure of porcine aminopeptidase-N with Arginine | |||||||||
Components | Aminopeptidase NAlanine aminopeptidase | |||||||||
Keywords | HYDROLASE / ZINC AMINOPEPTIDASE | |||||||||
Function / homology | Function and homology information membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / proteolysis / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | |||||||||
Authors | Chen, L. / Lin, Y.-L. / Li, F. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: The Rational Design of Therapeutic Peptides for Aminopeptidase N using a Substrate-Based Approach. Authors: Joshi, S. / Chen, L. / Winter, M.B. / Lin, Y.L. / Yang, Y. / Shapovalova, M. / Smith, P.M. / Liu, C. / Li, F. / LeBeau, A.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bv0.cif.gz | 420.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bv0.ent.gz | 340.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/6bv0 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/6bv0 | HTTPS FTP |
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-Related structure data
Related structure data | 6buyC 6bv1C 6bv2C 6bv3C 6bv4C 4fkeS 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 , 1 types, 1 molecules A
#1: Protein | Mass: 102692.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: ANPEP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P15145, membrane alanyl aminopeptidase |
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-Sugars , 3 types, 11 molecules
#2: Polysaccharide | #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 4 types, 870 molecules
#5: Chemical | ChemComp-ARG / | ||||
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#6: Chemical | ChemComp-SO4 / #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: 3.2 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 18% PEG3350, 200 MM LITHIUM SULFATE, 100 MM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 107699 / % possible obs: 98.2 % / Redundancy: 4.3 % / Rsym value: 0.075 / Net I/σ(I): 18.57 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.89 / Num. unique all: 9180 / Rsym value: 0.484 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FKE Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.425 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.143 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.463 Å2
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Refinement step | Cycle: 1 / Resolution: 1.86→50 Å
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Refine LS restraints |
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