+Open data
-Basic information
Entry | Database: PDB / ID: 1rf0 | ||||||
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Title | Crystal Structure of Fragment D of gammaE132A Fibrinogen | ||||||
Components |
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Keywords | BLOOD CLOTTING / BLOOD COAGULATION / FIBRINOGEN / FIBRINOGEN FRAGMENT D / RECOMBINANT FIBRINOGEN FRAGMENT D / RECOMBINANT FIBRINOGEN gammaE132A / fragment D of gammaE132A 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 / SYNCHROTRON / rigid body refinement / Resolution: 2.81 Å | ||||||
Authors | Kostelansky, M.S. / Gorkun, O.V. / Lord, S.T. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Calcium-Binding Site beta2, Adjacent to the "b" Polymerization Site, Modulates Lateral Aggregation of Protofibrils during Fibrin Polymerization. Authors: Kostelansky, M.S. / Lounes, K.C. / Ping, L.F. / Dickerson, S.K. / 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 | 1rf0.cif.gz | 275.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rf0.ent.gz | 221.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rf0_validation.pdf.gz | 502.3 KB | Display | wwPDB validaton report |
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Full document | 1rf0_full_validation.pdf.gz | 550.4 KB | Display | |
Data in XML | 1rf0_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 1rf0_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rf0 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rf0 | HTTPS FTP |
-Related structure data
Related structure data | 1rf1C 1lt9S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: Fibrinogen alpha/alpha-E Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGA / Plasmid: p767 / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02671 #2: Protein | Mass: 35940.215 Da / Num. of mol.: 2 / Fragment: Fibrinogen Bbeta Chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGB / Plasmid: p767 / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02675 #3: Protein | Mass: 35159.957 Da / Num. of mol.: 2 / Fragment: Fibrinogen gamma chain / Mutation: E132A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGG / Plasmid: p767 / Cell line (production host): CHO / Organ (production host): ovary / 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, 122 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: 3.03 Å3/Da / Density % sol: 59.38 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 14-15% PEG 3350, 70 mM calcium chloride, 2 mM sodium azide, 50 mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98389 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 11, 2003 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98389 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→18 Å / Num. all: 46581 / Num. obs: 46581 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 66 Å2 / Rsym value: 0.11 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.4 / Num. unique all: 4570 / Rsym value: 0.408 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 18 Å / Num. measured all: 186713 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.408 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: 1LT9 Resolution: 2.81→17.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1750722.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.0889 Å2 / ksol: 0.318139 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.81→17.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 18 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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