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Yorodumi- PDB-1zr0: Crystal Structure of Kunitz Domain 1 of Tissue Factor Pathway Inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zr0 | ||||||
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Title | Crystal Structure of Kunitz Domain 1 of Tissue Factor Pathway Inhibitor-2 with Bovine Trypsin | ||||||
Components |
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Keywords | HYDROLASE/BLOOD CLOTTING / serine protease / complex of serine protease-inhibitor / Kunitz type inhibitor / HYDROLASE-BLOOD CLOTTING COMPLEX | ||||||
Function / homology | Function and homology information cellular response to fluid shear stress / extracellular matrix structural constituent / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / extracellular matrix / serine-type endopeptidase inhibitor activity / blood coagulation / endopeptidase activity ...cellular response to fluid shear stress / extracellular matrix structural constituent / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / extracellular matrix / serine-type endopeptidase inhibitor activity / blood coagulation / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Schmidt, A.E. / Chand, H.S. / Cascio, D. / Kisiel, W. / Bajaj, S.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structure of Kunitz domain 1 (KD1) of tissue factor pathway inhibitor-2 in complex with trypsin. Implications for KD1 specificity of inhibition Authors: Schmidt, A.E. / Chand, H.S. / Cascio, D. / Kisiel, W. / Bajaj, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zr0.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zr0.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/1zr0 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/1zr0 | HTTPS FTP |
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-Related structure data
Related structure data | 1tawS 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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2 |
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Unit cell |
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Details | Biological assembly consists of one trypsin molecule and one KD1 molecule in complex. |
-Components
#1: Protein | Mass: 23310.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin #2: Protein | Mass: 7376.205 Da / Num. of mol.: 2 / Fragment: Kunitz domain 1 (KD1) Source method: isolated from a genetically manipulated source Details: numbered according to the BPTI numbering system / Source: (gene. exp.) Homo sapiens (human) / Gene: TFPI2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P48307 #3: Chemical | #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: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Hepes, ammonium sulfate, calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2004 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.802→90 Å / Num. all: 63596 / Num. obs: 60093 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.802→1.847 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 6.9 / Num. unique all: 4484 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TAW Resolution: 1.802→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.802→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.847 Å
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