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Yorodumi- PDB-1j35: Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j35 | ||||||
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Title | Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein | ||||||
Components |
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Keywords | Protein binding/Blood clotting / MAGNESIUM ION / CALCIUM ION / GLA DOMAIN / Protein binding-Blood clotting COMPLEX | ||||||
Function / homology | Function and homology information coagulation factor IXa / zymogen activation / blood coagulation / signaling receptor activity / toxin activity / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / magnesium ion binding ...coagulation factor IXa / zymogen activation / blood coagulation / signaling receptor activity / toxin activity / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / magnesium ion binding / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Trimeresurus flavoviridis (habu) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shikamoto, Y. / Morita, T. / Fujimoto, Z. / Mizuno, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structure of Mg2+- and Ca2+-bound Gla Domain of Factor IX Complexed with Binding Protein Authors: Shikamoto, Y. / Morita, T. / Fujimoto, Z. / Mizuno, H. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X Authors: Mizuno, H. / Fujimoto, Z. / Atoda, H. / Morita, T. #2: Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of coagulation factor IX-binding protein from habu snake venom at 2.6 A: implication of central loop swapping based on deletion in the linker region Authors: Mizuno, H. / Fujimoto, Z. / Koizumi, M. / Kano, H. / Atoda, H. / Morita, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j35.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j35.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1j35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j35_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 1j35_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 1j35_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1j35_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j35 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j35 | HTTPS FTP |
-Related structure data
Related structure data | 1j34C 1iodS 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: 14655.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: venom / References: UniProt: P23806, UniProt: Q7LZ71*PLUS | ||
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#2: Protein | Mass: 14455.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: venom / References: UniProt: P23807 | ||
#3: Protein/peptide | Mass: 6177.313 Da / Num. of mol.: 1 / Fragment: GLA DOMAIN / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: plasma / References: UniProt: P00741, coagulation factor IXa | ||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.3 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8 Details: PEG 6000, Tris-HCl, calcium chloride, pH 8, MICROBATCH, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL41XU / Wavelength: 0.72 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 27532 / Num. obs: 27532 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.88 Å / Rmerge(I) obs: 0.252 / Num. unique all: 2639 / % possible all: 72.4 |
Reflection | *PLUS % possible obs: 94 % |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IOD Resolution: 1.8→19.54 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 445935.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.8158 Å2 / ksol: 0.321533 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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