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Yorodumi- PDB-1kwm: Human procarboxypeptidase B: Three-dimensional structure and impl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kwm | ||||||
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Title | Human procarboxypeptidase B: Three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI) | ||||||
Components | Procarboxypeptidase B | ||||||
Keywords | HYDROLASE / Procarboxypeptidase B | ||||||
Function / homology | Function and homology information carboxypeptidase B / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Pereira, P.J.B. / Segura-Martin, S. / Ferrer-Orta, C. / Vendrell, J. / Aviles, F.-X. / Coll, M. / Gomis-Rueth, F.-X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI). Authors: Barbosa Pereira, P.J. / Segura-Martin, S. / Oliva, B. / Ferrer-Orta, C. / Aviles, F.X. / Coll, M. / Gomis-Ruth, F.X. / Vendrell, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kwm.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kwm.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kwm_validation.pdf.gz | 397.8 KB | Display | wwPDB validaton report |
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Full document | 1kwm_full_validation.pdf.gz | 404.6 KB | Display | |
Data in XML | 1kwm_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1kwm_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kwm ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kwm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45955.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / References: UniProt: P15086, carboxypeptidase B #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, sodium citrate, sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.97935 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→27.4 Å / Num. all: 104805 / Num. obs: 104805 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.05 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.6→1.68 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.241 / % possible all: 81.9 |
Reflection | *PLUS Highest resolution: 1.6 Å / Redundancy: 2.9 % / Num. measured all: 303465 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 81.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.241 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.4 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→27.4 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.136 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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