+Open data
-Basic information
Entry | Database: PDB / ID: 1re4 | ||||||
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Title | Crystal Structure of Fragment D of BbetaD398A Fibrinogen | ||||||
Components |
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Keywords | BLOOD CLOTTING / RECOMBINANT FIBRINOGEN FRAGMENT D / RECOMBINANT FIBRINOGEN / Mutant fibrinogen / variant fibrinogen / BbetaD398A 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: 2.7 Å | ||||||
Authors | Kostelansky, M.S. / Betts, L. / Gorkun, O.V. / Lord, S.T. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: BbetaGlu397 and BbetaAsp398 but not BbetaAsp432 are required for "B:b" interactions. Authors: Kostelansky, M.S. / Bolliger-Stucki, B. / 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 | 1re4.cif.gz | 275.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1re4.ent.gz | 221.3 KB | Display | PDB format |
PDBx/mmJSON format | 1re4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1re4_validation.pdf.gz | 505.1 KB | Display | wwPDB validaton report |
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Full document | 1re4_full_validation.pdf.gz | 553.8 KB | Display | |
Data in XML | 1re4_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 1re4_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/1re4 ftp://data.pdbj.org/pub/pdb/validation_reports/re/1re4 | HTTPS FTP |
-Related structure data
Related structure data | 1re3C 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: Fragment D of fibrinogen alpha chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGA / Plasmid: pMLP / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02671 #2: Protein | Mass: 35896.207 Da / Num. of mol.: 2 / Fragment: Fragment D of BbetaD398A fibrinogen beta chain / Mutation: D398A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGB / Plasmid: pMLP / Cell line (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02675 #3: Protein | Mass: 35217.992 Da / Num. of mol.: 2 / Fragment: Fragment D of fibrinogen gamma chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGG / Plasmid: pMLP / 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, 170 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: 3.01 Å3/Da / Density % sol: 59.14 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97956 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Feb 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97956 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→18 Å / Num. all: 47513 / Num. obs: 47513 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 50.2 Å2 / Rsym value: 0.111 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1.8 / Num. unique all: 4798 / Rsym value: 0.482 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: PDB entry 1LT9 Resolution: 2.7→17.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2071770.98 / 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: 32.8296 Å2 / ksol: 0.323915 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→17.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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