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Yorodumi- PDB-4kx9: Crystal structure of human aminopeptidase A complexed with arginine -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kx9 | |||||||||
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Title | Crystal structure of human aminopeptidase A complexed with arginine | |||||||||
Components | Glutamyl aminopeptidase | |||||||||
Keywords | HYDROLASE / zinc-aminopeptidase | |||||||||
Function / homology | Function and homology information glutamyl aminopeptidase / glomerulus development / peptide catabolic process / brush border / metalloaminopeptidase activity / 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 / brush border / metalloaminopeptidase activity / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 | 4kx9.cif.gz | 412.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kx9.ent.gz | 341.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kx9_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4kx9_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4kx9_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 4kx9_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/4kx9 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/4kx9 | HTTPS FTP |
-Related structure data
Related structure data | 4kx7C 4kx8C 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 on special symmetry positions |
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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 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | #5: Sugar | |
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-Non-polymers , 3 types, 616 molecules
#4: Chemical | ChemComp-ZN / |
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#6: Chemical | ChemComp-ARG / |
#7: 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: 3.38 Å3/Da / Density % sol: 63.64 % |
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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: Jul 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 67214 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→45.59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.325 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.191 / 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: 36.256 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→45.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.373 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -12.8827 Å / Origin y: 42.0914 Å / Origin z: 37.4878 Å
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Refinement TLS group |
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