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- PDB-1nl0: Crystal structure of human factor IX Gla domain in complex of an ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nl0 | ||||||
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Title | Crystal structure of human factor IX Gla domain in complex of an inhibitory antibody, 10C12 | ||||||
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![]() | IMMUNE SYSTEM / ANTIBODY / GLA DOMAIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, M. / Furie, B.C. / Furie, B. | ||||||
![]() | ![]() Title: Crystal Structure of the Calcium-stabilized Human Factor IX Gla Domain Bound to a Conformation-specific Anti-factor IX Antibody. Authors: Huang, M. / Furie, B.C. / Furie, B. | ||||||
History |
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Remark 999 | SEQUENCE an appropriate sequence database reference was not available for chains L and H at the ...SEQUENCE an appropriate sequence database reference was not available for chains L and H at the time of processing. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.3 KB | Display | ![]() |
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PDB format | ![]() | 83.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules G
#3: Protein | Mass: 7117.892 Da / Num. of mol.: 1 / Fragment: Gla domain / Source method: obtained synthetically Details: The protein was chemically synthesized. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS. References: UniProt: P00740 |
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-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 22631.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23800.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 155 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / | ||
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#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.66 Å / Num. obs: 28585 / % possible obs: 81.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 5.4 / % possible all: 38.7 |
Reflection | *PLUS Num. measured all: 241036 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 38.7 % / Num. unique obs: 1353 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: homology model from swissmodel Resolution: 2.2→24.66 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2183458.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4155 Å2 / ksol: 0.378478 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
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Refine analyze | Luzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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