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- PDB-1ten: STRUCTURE OF A FIBRONECTIN TYPE III DOMAIN FROM TENASCIN PHASED B... -

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Basic information

Entry
Database: PDB / ID: 1ten
TitleSTRUCTURE OF A FIBRONECTIN TYPE III DOMAIN FROM TENASCIN PHASED BY MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN
ComponentsTENASCIN
KeywordsCELL ADHESION PROTEIN
Function / homology
Function and homology information


perisynaptic extracellular matrix / tenascin complex / interstitial matrix / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / cellular response to prostaglandin D stimulus / syndecan binding / response to fibroblast growth factor / cellular response to vitamin D ...perisynaptic extracellular matrix / tenascin complex / interstitial matrix / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / cellular response to prostaglandin D stimulus / syndecan binding / response to fibroblast growth factor / cellular response to vitamin D / prostate gland epithelium morphogenesis / negative regulation of cell adhesion / extracellular matrix structural constituent / neuromuscular junction development / Syndecan interactions / odontogenesis of dentin-containing tooth / basement membrane / ECM proteoglycans / Integrin cell surface interactions / regulation of cell adhesion / response to mechanical stimulus / cellular response to retinoic acid / regulation of cell migration / morphogenesis of an epithelium / regulation of cell growth / Post-translational protein phosphorylation / response to wounding / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / regulation of inflammatory response / response to ethanol / collagen-containing extracellular matrix / cell adhesion / endoplasmic reticulum lumen / focal adhesion / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / membrane
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF domain / 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. / EGF-like domain, extracellular / EGF-like domain ...Tenascin, EGF-like domain / Tenascin EGF domain / 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. / EGF-like domain, extracellular / EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLeahy, D.J. / Hendrickson, W.A. / Aukhil, I. / Erickson, H.P.
CitationJournal: Science / Year: 1992
Title: Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein.
Authors: Leahy, D.J. / Hendrickson, W.A. / Aukhil, I. / Erickson, H.P.
History
DepositionAug 28, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TENASCIN


Theoretical massNumber of molelcules
Total (without water)10,0611
Polymers10,0611
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.780, 49.780, 71.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUES 841, 871, 880, 888, AND 890 ARE DISORDERED.
Components on special symmetry positions
IDModelComponents
11A-937-

HOH

21A-959-

HOH

31A-961-

HOH

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Components

#1: Protein TENASCIN


Mass: 10061.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P24821
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES ARE NUMBERED ACCORDING TO NIES ET AL. (1991), J. BIOL. CHEM., 266, P. 2818.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 %PEG33501reservoir
210 mMcitric acid1reservoir
310-20 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 7950 / Observed criterion σ(F): 3 / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→10 Å / Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms865 0 0 216 1081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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