+Open data
-Basic information
Entry | Database: PDB / ID: 1fzb | ||||||
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Title | CRYSTAL STRUCTURE OF CROSSLINKED FRAGMENT D | ||||||
Components |
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Keywords | BLOOD COAGULATION / PLASMA / PLATELET / FIBRINOGEN / FIBRIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Spraggon, G. / Everse, S.J. / Doolittle, R.F. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Crystal structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin. Authors: Spraggon, G. / Everse, S.J. / Doolittle, R.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fzb.cif.gz | 292.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fzb.ent.gz | 236.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fzb_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 1fzb_full_validation.pdf.gz | 504 KB | Display | |
Data in XML | 1fzb_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 1fzb_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fzb ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.665601, 0.189776, -0.721775), Vector: |
-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 10244.963 Da / Num. of mol.: 2 / Fragment: DOUBLE FRAGMENT D / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P02671 #2: Protein | Mass: 37691.992 Da / Num. of mol.: 2 / Fragment: DOUBLE FRAGMENT D / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P02675 #3: Protein | Mass: 36223.281 Da / Num. of mol.: 2 / Fragment: DOUBLE FRAGMENT D / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P02679 |
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-Protein/peptide / Sugars / Non-polymers , 3 types, 6 molecules GH
#4: Protein/peptide | Mass: 426.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: BOUND PEPTIDE CAUSES THE FIBRIN CLOT CONFORMATION #5: Sugar | #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.93 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 13-14% PEG 3350, 50 MM TRIS PH 7.0, 10 MM CALCIUM CHLORIDE 1MM SODIUM AZIDE 5MM GLY-PRO-ARG-PRO-AMIDE | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
Detector | Date: Sep 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 40637 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.192 |
Reflection | *PLUS Num. measured all: 244386 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FIBRINOGEN FRAGMENT D Resolution: 2.9→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 30.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |