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Yorodumi- PDB-4ajt: The crystal structure of mouse protein-Z dependent protease inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ajt | ||||||
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Title | The crystal structure of mouse protein-Z dependent protease inhibitor(mZPI) | ||||||
Components | PROTEIN Z-DEPENDENT PROTEASE INHIBITOR | ||||||
Keywords | BLOOD CLOTTING / ZPI | ||||||
Function / homology | Function and homology information Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / liver regeneration / serine-type endopeptidase inhibitor activity / blood coagulation / heparin binding / extracellular space Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yan, Y. / Zhou, A. | ||||||
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 | 4ajt.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ajt.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ajt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ajt_validation.pdf.gz | 419.1 KB | Display | wwPDB validaton report |
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Full document | 4ajt_full_validation.pdf.gz | 421.9 KB | Display | |
Data in XML | 4ajt_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4ajt_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/4ajt ftp://data.pdbj.org/pub/pdb/validation_reports/aj/4ajt | HTTPS FTP |
-Related structure data
Related structure data | 4afxC 4ajuC 3f1sS S: Starting model for refinement C: citing same article (ref.) |
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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: 49512.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q8R121 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.7 % / Description: NONE |
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Crystal grow | pH: 7.2 / Details: 4.3 M NACL,0.1 M HEPES-NA, PH7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 |
Detector | Date: Feb 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→72.34 Å / Num. obs: 23621 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.6 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3F1S Resolution: 2.5→72.34 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 28.141 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.247 / 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: 57.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→72.34 Å
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Refine LS restraints |
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