[English] 日本語
Yorodumi- PDB-6rfk: Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rfk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant) | ||||||
Components |
| ||||||
Keywords | HYDROLASE | ||||||
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 / endopeptidase activity / collagen-containing extracellular matrix / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Huntington, J.A. / Sendall, T.J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: NMR resonance assignments of apo and EGRCK-inhibited factor IXa Authors: Sendall, T.J. / Huntington, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rfk.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rfk.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rfk_validation.pdf.gz | 719.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rfk_full_validation.pdf.gz | 734.6 KB | Display | |
Data in XML | 6rfk_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6rfk_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/6rfk ftp://data.pdbj.org/pub/pdb/validation_reports/rf/6rfk | HTTPS FTP |
-Related structure data
Related structure data | 5jb8S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Coagulation factor ... , 2 types, 2 molecules ES
#1: Protein | Mass: 6841.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: E. coli expression construct replaces the Leu at the beginning of the EGF2 domain with Met. Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa |
---|---|
#2: Protein | Mass: 26160.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Mutated at K148 and R150 to Q to prevent autolysis. Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa |
-Protein/peptide , 1 types, 1 molecules I
#3: Protein/peptide | |
---|
-Non-polymers , 4 types, 236 molecules
#4: Chemical | ChemComp-B3P / | ||
---|---|---|---|
#5: Chemical | ChemComp-CA / | ||
#6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 0.1M BIS-TRIS propane pH 8.5, 24% PEG 3350, 0.275M Na Malonate PH range: 8-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Aug 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→70.82 Å / Num. obs: 61775 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 2963 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JB8 Resolution: 1.6→70.82 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 3.013 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.236 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→70.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|