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Yorodumi- PDB-4afx: Crystal structure of the reactive loop cleaved ZPI in I2 space group -
+Open data
-Basic information
Entry | Database: PDB / ID: 4afx | ||||||
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Title | Crystal structure of the reactive loop cleaved ZPI in I2 space group | ||||||
Components | (PROTEIN Z DEPENDENT PROTEASE ...) x 2 | ||||||
Keywords | HYDROLASE INHIBITOR / SERPIN / PROTEIN Z DEPENDENT INHIBITOR / COAGULATION | ||||||
Function / homology | Function and homology information liver regeneration / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / endoplasmic reticulum lumen / extracellular space / extracellular exosome Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Zhou, A. / Yan, Y. / Wei, Z. | ||||||
Citation | Journal: Blood / Year: 2012 Title: Structural Basis for Catalytic Activation of Protein Z-Dependent Protease Inhibitor (Zpi) by Protein Z. Authors: Huang, X. / Yan, Y. / Tu, Y. / Gatti, J. / Broze, G.J.J. / Zhou, A. / Olson, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4afx.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4afx.ent.gz | 132.5 KB | Display | PDB format |
PDBx/mmJSON format | 4afx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/4afx ftp://data.pdbj.org/pub/pdb/validation_reports/af/4afx | HTTPS FTP |
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-Related structure data
Related structure data | 4ajtC 4ajuC 7apiS C: citing same article (ref.) 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
-PROTEIN Z DEPENDENT PROTEASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 44357.996 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-408 / Mutation: YES Source method: isolated from a genetically manipulated source Details: REACTIVE LOOP CLEAVED ZPI / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-HZPI-Y387R / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9UK55 |
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#2: Protein/peptide | Mass: 4167.010 Da / Num. of mol.: 1 / Fragment: RESIDUES 409-444 / Mutation: YES Source method: isolated from a genetically manipulated source Details: REACTIVE LOOP CLEAVED ZPI / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-HZPI-Y387R / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9UK55 |
-Non-polymers , 4 types, 33 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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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: 45 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 1.8M NAK PHOSPHATE, PH5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→44.39 Å / Num. obs: 31054 / % possible obs: 84.3 % / Observed criterion σ(I): 2 / Redundancy: 87 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.09→2.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.8 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7API Resolution: 2.09→66.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.127 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.182 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.827 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→66.52 Å
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Refine LS restraints |
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