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- PDB-1dug: STRUCTURE OF THE FIBRINOGEN G CHAIN INTEGRIN BINDING AND FACTOR X... -

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Basic information

Entry
Database: PDB / ID: 1dug
TitleSTRUCTURE OF THE FIBRINOGEN G CHAIN INTEGRIN BINDING AND FACTOR XIIIA CROSSLINKING SITES OBTAINED THROUGH CARRIER PROTEIN DRIVEN CRYSTALLIZATION
Componentschimera of GLUTATHIONE S-TRANSFERASE-synthetic LINKEr-C-TERMINAL FIBRINOGEN GAMMA CHAIN
Keywordstransferase / blood clotting / gamma chain integrin fragment / carrier protein driven crystallization
Function / homology
Function and homology information


platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / platelet alpha granule / 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 ...platelet maturation / fibrinogen complex / Regulation of TLR by endogenous ligand / blood coagulation, fibrin clot formation / platelet alpha granule / 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 / glutathione transferase / glutathione transferase activity / protein secretion / protein polymerization / Integrin cell surface interactions / cellular response to interleukin-1 / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of vasoconstriction / fibrinolysis / cell adhesion molecule binding / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / Post-translational protein phosphorylation / positive regulation of protein secretion / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / 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 / Signaling by BRAF and RAF1 fusions / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / blood microparticle / positive regulation of ERK1 and ERK2 cascade / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / structural molecule activity / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Fibrinogen gamma chain / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsWare, S. / Donahue, J.P. / Hawiger, J. / Anderson, W.F.
CitationJournal: Protein Sci. / Year: 1999
Title: Structure of the fibrinogen gamma-chain integrin binding and factor XIIIa cross-linking sites obtained through carrier protein driven crystallization.
Authors: Ware, S. / Donahue, J.P. / Hawiger, J. / Anderson, W.F.
History
DepositionJan 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimera of GLUTATHIONE S-TRANSFERASE-synthetic LINKEr-C-TERMINAL FIBRINOGEN GAMMA CHAIN
B: chimera of GLUTATHIONE S-TRANSFERASE-synthetic LINKEr-C-TERMINAL FIBRINOGEN GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8814
Polymers54,2672
Non-polymers6152
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.78, 105.78, 137.23
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein chimera of GLUTATHIONE S-TRANSFERASE-synthetic LINKEr-C-TERMINAL FIBRINOGEN GAMMA CHAIN


Mass: 27133.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GLUTATHIONE S-TRANSFERASE (residues 1-217) bound to synthetic SDP linker (residues 218-220) bound to C-TERMINAL FIBRINOGEN GAMMA CHAIN (residues 221-234)
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Homo sapiens (human)
Description: EUKARYOTA; METAZOA; PLATYHELMINTHES; TREMATODA; DIGENEA; STRIGEIDIDA; SCHISTOSO MATOIDEA; SCHISTOSOMATIDAE; SCHISTOSOMA
Gene: FGG,PRO2061 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA
References: UniProt: P08515, UniProt: P02679, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, sodium acetate, sodium chloride, ammonium sulfate, Tris, reduced glutathione, pH 4.6, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: -170 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
28 %PEG33501drop
350 mMsodium acetate1drop
425 mMsodium chloride1drop
517.5 mMammonium sulfate1drop
65 mMTris-HCl1drop
75 mMglutathinoe1drop
816 %PEG33501reservoir
9100 mMsodium acetate1reservoir
1035 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0093
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 1.7→28 Å / Num. all: 376772 / Num. obs: 67736 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.56 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 1.8→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.25 / Num. unique all: 12570 / % possible all: 66.1
Reflection
*PLUS
Num. measured all: 376772
Reflection shell
*PLUS
% possible obs: 66.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→28 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 5745 -RANDOM
Rwork0.185 ---
obs0.185 57456 89.2 %-
all-67736 --
Refinement stepCycle: LAST / Resolution: 1.8→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 40 662 4520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.425
X-RAY DIFFRACTIONx_bond_d0.007

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