+Open data
-Basic information
Entry | Database: PDB / ID: 1rfn | ||||||
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Title | HUMAN COAGULATION FACTOR IXA IN COMPLEX WITH P-AMINO BENZAMIDINE | ||||||
Components | (PROTEIN (COAGULATION FACTOR ...) x 2 | ||||||
Keywords | COAGULATION FACTOR / SERINE PROTEINASE / BLOOD COAGULATION | ||||||
Function / homology | Function and homology information Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation ...Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Hopfner, K.-P. / Lang, A. / Karcher, A. / Sichler, K. / Kopetzki, E. / Brandstetter, H. / Huber, R. / Bode, W. / Engh, R.A. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Coagulation factor IXa: the relaxed conformation of Tyr99 blocks substrate binding. Authors: Hopfner, K.P. / Lang, A. / Karcher, A. / Sichler, K. / Kopetzki, E. / Brandstetter, H. / Huber, R. / Bode, W. / Engh, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rfn.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rfn.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rfn ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rfn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-PROTEIN (COAGULATION FACTOR ... , 2 types, 2 molecules AB
#1: Protein | Mass: 26190.818 Da / Num. of mol.: 1 / Fragment: FRAGMENT EGF2-CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: P00740 |
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#2: Protein | Mass: 6256.135 Da / Num. of mol.: 1 / Fragment: FRAGMENT EGF2-CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: P00740 |
-Non-polymers , 4 types, 19 molecules
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-PBZ / |
#5: Chemical | ChemComp-TBU / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 16348 / % possible obs: 92.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.077 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 92.7 % / Redundancy: 2.2 % |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.93 Å / % possible obs: 82 % / Rmerge(I) obs: 0.316 |
-Processing
Software | Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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Software | *PLUS Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 25 Å / Rfactor obs: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |