+Open data
-Basic information
Entry | Database: PDB / ID: 4kx7 | |||||||||
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Title | Crystal structure of human aminopeptidase A | |||||||||
Components | Glutamyl aminopeptidase | |||||||||
Keywords | HYDROLASE / zinc-aminopeptidase fold | |||||||||
Function / homology | Function and homology information glutamyl aminopeptidase / glomerulus development / peptide catabolic process / metalloaminopeptidase activity / brush border / regulation of systemic arterial blood pressure by renin-angiotensin / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / aminopeptidase activity / peptide binding ...glutamyl aminopeptidase / glomerulus development / peptide catabolic process / metalloaminopeptidase activity / brush border / regulation of systemic arterial blood pressure by renin-angiotensin / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / aminopeptidase activity / peptide binding / regulation of blood pressure / cell migration / apical part of cell / cell-cell signaling / cytoplasmic vesicle / angiogenesis / cell population proliferation / apical plasma membrane / lysosomal membrane / external side of plasma membrane / proteolysis / extracellular space / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å | |||||||||
Authors | Yang, Y. / Liu, C. / Lin, Y.Y. / Li, F. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural insights into central hypertension regulation by human aminopeptidase a. Authors: Yang, Y. / Liu, C. / Lin, Y.L. / Li, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kx7.cif.gz | 409.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kx7.ent.gz | 340.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kx7_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4kx7_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4kx7_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 4kx7_validation.cif.gz | 59 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/4kx7 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/4kx7 | HTTPS FTP |
-Related structure data
Related structure data | 4kx8C 4kx9C 4kxaC 4kxbC 4kxcC 4kxdC 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: 102719.477 Da / Num. of mol.: 1 / Fragment: UNP residues 76-957 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ENPEP / Plasmid: pFastBacTM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q07075, glutamyl aminopeptidase |
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-Sugars , 3 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | #5: Sugar | |
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-Non-polymers , 2 types, 595 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: 3.39 Å3/Da / Density % sol: 63.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.6 M sodium citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 |
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Detector | Date: May 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 72327 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MIR / Resolution: 2.15→38.86 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 13.773 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 2.895 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.962 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→38.86 Å
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