[English] 日本語
Yorodumi- PDB-1zhm: Crystal Structure of the Catalytic Domain of the Coagulation Fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zhm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Catalytic Domain of the Coagulation Factor XIa in Complex with Benzamidine (S434A-T475A-K437 Mutant) | ||||||
Components | coagulation factor XIFactor XI | ||||||
Keywords | HYDROLASE / BLOOD CLOTTING / Factor XI / benzamidine | ||||||
Function / homology | Function and homology information coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Jin, L. / Pandey, P. / Babine, R.E. / Weaver, D.T. / Abdel-Meguid, S.S. / Strickler, J.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Mutation of surface residues to promote crystallization of activated factor XI as a complex with benzamidine: an essential step for the iterative structure-based design of factor XI inhibitors. Authors: Jin, L. / Pandey, P. / Babine, R.E. / Weaver, D.T. / Abdel-Meguid, S.S. / Strickler, J.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zhm.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zhm.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/1zhm ftp://data.pdbj.org/pub/pdb/validation_reports/zh/1zhm | HTTPS FTP |
---|
-Related structure data
Related structure data | 1zhpC 1zhrC 1xx9S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26768.434 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: S434A, T475A, K437A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Cell line (production host): X-33 / Production host: Pichia pastoris (fungus) / References: UniProt: P03951, coagulation factor XIa |
---|---|
#2: Chemical | ChemComp-BEN / |
#3: Chemical | ChemComp-GSH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % |
---|---|
Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ammonium Sulfate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 14, 2001 / Details: Monochromator |
Radiation | Monochromator: channel-cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 20831 / Num. obs: 20831 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.96→2.03 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 6.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XX9, chain A Resolution: 1.96→37.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 198424.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.47 Å2 / ksol: 0.382448 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→37.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.96→2.03 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|