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Yorodumi- PDB-2nsm: Crystal structure of the human carboxypeptidase N (Kininase I) ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nsm | ||||||
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Title | Crystal structure of the human carboxypeptidase N (Kininase I) catalytic domain | ||||||
Components | Carboxypeptidase N catalytic chain | ||||||
Keywords | HYDROLASE / caroxypeptidase / zinc peptidase / transthyretin-like domain / hormone processing / peptide modification | ||||||
Function / homology | Function and homology information lysine carboxypeptidase / peptide metabolic process / regulation of complement activation / bradykinin catabolic process / metallocarboxypeptidase activity / response to glucocorticoid / Regulation of Complement cascade / protein processing / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Keil, C. / Maskos, K. / Than, M. / Hoopes, J.T. / Huber, R. / Tan, F. / Deddish, P.A. / Erdoes, E.G. / Skidgel, R.A. / Bode, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal structure of the human carboxypeptidase N (kininase I) catalytic domain Authors: Keil, C. / Maskos, K. / Than, M. / Hoopes, J.T. / Huber, R. / Tan, F. / Deddish, P.A. / Erdoes, E.G. / Skidgel, R.A. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nsm.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nsm.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 2nsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/2nsm ftp://data.pdbj.org/pub/pdb/validation_reports/ns/2nsm | HTTPS FTP |
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-Related structure data
Related structure data | 1h8lS S: Starting model for refinement |
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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
#1: Protein | Mass: 50184.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P15169, lysine carboxypeptidase | ||||
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#2: Sugar | #3: Chemical | ChemComp-SO4 / #4: 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: 3.55 Å3/Da / Density % sol: 65.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes, 2M Ammonium sulfate, 5mM EDTA, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal, non dispersive / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 41723 / Num. obs: 41723 / % possible obs: 99.4 % / Observed criterion σ(F): 4.37 / Observed criterion σ(I): 4.37 / Redundancy: 3.36 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 15.26 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.37 / Num. unique all: 41723 / Rsym value: 0.28 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1H8L Resolution: 2.1→20 Å / σ(F): 4.37 / σ(I): 4.37 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.1 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.012
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