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Yorodumi- PDB-6f4u: Crystal structure of reactive loop cleaved kallistatin at 1.9 ang... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f4u | |||||||||
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Title | Crystal structure of reactive loop cleaved kallistatin at 1.9 angstrom resolution | |||||||||
Components | (Kallistatin) x 2 | |||||||||
Keywords | HYDROLASE / inhibitor / Serpin / kallekrein / kallistatin | |||||||||
Function / homology | Function and homology information platelet dense granule lumen / serine-type endopeptidase inhibitor activity / Platelet degranulation / extracellular space / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | |||||||||
Authors | Zhou, A. / Wei, Z. / Lin, F. | |||||||||
Funding support | United Kingdom, China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of human Kallistatin Authors: Zhou, A. / Ma, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f4u.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f4u.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 6f4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/6f4u ftp://data.pdbj.org/pub/pdb/validation_reports/f4/6f4u | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AD
#1: Protein | Mass: 39031.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: reactive loop cleaved human kallistatin with an Extra Gly at the N-terminus Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA4, KST, PI4 / Plasmid: Psumo3-Kal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29622 |
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#2: Protein/peptide | Mass: 4568.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: reactive loop cleaved human kallistatin with an Extra Gly at the N-terminus Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA4, KST, PI4 / Plasmid: Psumo3-Kal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29622 |
-Non-polymers , 5 types, 201 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-NA / | #7: 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: 3.25 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% tertbutanal |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.196 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jan 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.196 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.67 Å / Num. obs: 44414 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6433 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Resolution: 1.9→98.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.288 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.154 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→98.5 Å
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