+Open data
-Basic information
Entry | Database: PDB / ID: 2wph | ||||||
---|---|---|---|---|---|---|---|
Title | factor IXa superactive triple mutant | ||||||
Components |
| ||||||
Keywords | BLOOD CLOTTING / HYDROLASE / GLYCOPROTEIN / HEMOSTASIS | ||||||
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) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Zogg, T. / Brandstetter, H. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structural Basis of the Cofactor- and Substrate-Assisted Activation of Human Coagulation Factor Ixa Authors: Zogg, T. / Brandstetter, H. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "SA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "SA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "SB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wph.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wph.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wph_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wph_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 2wph_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 2wph_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/2wph ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wph | HTTPS FTP |
-Related structure data
Related structure data | 2wpiC 2wpjC 2wpkC 2wplC 2wpmC 1rfnS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-COAGULATION FACTOR IXA ... , 2 types, 2 molecules ES
#1: Protein | Mass: 6496.395 Da / Num. of mol.: 1 / Fragment: EGF2 DOMAIN, RESIDUES 133-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-FIXA-3X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00740, coagulation factor IXa |
---|---|
#3: Protein | Mass: 26084.672 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 227-461 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-FIXA-3X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00740, coagulation factor IXa |
-Protein/peptide , 1 types, 1 molecules L
#2: Protein/peptide | |
---|
-Non-polymers , 3 types, 527 molecules
#4: Chemical | ChemComp-CA / | ||
---|---|---|---|
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 30.68 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: 22 % PEG 3000, 100 MM BIS/TRIS, PH 6.85 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 13, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→7 Å / Num. obs: 44244 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 81 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RFN Resolution: 1.5→7 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 58.07 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.48→1.55 Å / Total num. of bins used: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|