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- PDB-7cj1: The crystal structure of FXIa serine protease domain in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cj1 | ||||||
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Title | The crystal structure of FXIa serine protease domain in complex with benzamidine | ||||||
![]() | Coagulation factor XI | ||||||
![]() | HYDROLASE / Factor XI / Blood coagulation | ||||||
Function / homology | ![]() 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, L. / Huang, M. | ||||||
![]() | ![]() Title: The crystal structure of FXIa serine protease domain in complex with benzamidine. Authors: Jiang, L. / Huang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.9 KB | Display | ![]() |
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PDB format | ![]() | 156.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zhrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: 16 - 243 / Label seq-ID: 1 - 236
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Components
#1: Protein | Mass: 26714.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-BEN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 25% PEG2000 MME, 0.1 M Tris-Hcl pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 3→99 Å / Num. obs: 16815 / % possible obs: 92.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.133 / Num. unique obs: 639 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZHR Resolution: 3→60 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.823 / SU B: 23.241 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.582 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.42 Å2 / Biso mean: 15.74 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 3→60 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3→3.08 Å /
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