+Open data
-Basic information
Entry | Database: PDB / ID: 1lt9 | ||||||
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Title | Crystal Structure of Recombinant Human Fibrinogen Fragment D | ||||||
Components |
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Keywords | BLOOD CLOTTING / blood coagulation / fibrinogen / fibrinogen fragment D / recombinant fibrinogen fragment D / recombinant fibrinogen | ||||||
Function / homology | Function and homology information platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...platelet maturation / blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein secretion / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / cell adhesion molecule binding / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kostelansky, M.S. / Betts, L. / Gorkun, O.V. / Lord, S.T. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: 2.8 A Crystal Structures of Recombinant Fibrinogen Fragment D with and without Two Peptide Ligands: GHRP Binding to the "b" Site Disrupts Its Nearby Calcium-binding Site. Authors: Kostelansky, M.S. / Betts, L. / Gorkun, O.V. / Lord, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lt9.cif.gz | 266.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lt9.ent.gz | 218.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lt9_validation.pdf.gz | 505.3 KB | Display | wwPDB validaton report |
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Full document | 1lt9_full_validation.pdf.gz | 552.1 KB | Display | |
Data in XML | 1lt9_validation.xml.gz | 53.2 KB | Display | |
Data in CIF | 1lt9_validation.cif.gz | 72.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1lt9 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1lt9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 7747.030 Da / Num. of mol.: 2 / Fragment: Fragment D (residues 126-191) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02671 #2: Protein | Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Fragment D (residues 149-461) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02675 #3: Protein | Mass: 35217.992 Da / Num. of mol.: 2 / Fragment: Fragment D (residues 96-406) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02679 |
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-Sugars , 1 types, 2 molecules
#4: Sugar |
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-Non-polymers , 2 types, 152 molecules
#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.22 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 9% PEG 3350, 70mM Calcium Chloride, 2mM Sodium Azide, 50mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 27, 2001 / Details: Osmic Confocal Blue Multilayer Optics |
Radiation | Monochromator: Osmic Confocal Blue Multilayer Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→18 Å / Num. all: 47742 / Num. obs: 47742 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 70.6 Å2 / Rsym value: 0.11 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 4684 / Rsym value: 0.54 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 18 Å / Num. measured all: 217604 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→17.98 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.6846 Å2 / ksol: 0.30323 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.44 Å / Luzzati sigma a free: 0.48 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→17.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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