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- PDB-1rjh: Structure of the Calcium Free Form of the C-type Lectin-like Doma... -

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Basic information

Entry
Database: PDB / ID: 1rjh
TitleStructure of the Calcium Free Form of the C-type Lectin-like Domain of Tetranectin
ComponentsTetranectin
KeywordsPROTEIN BINDING / Apo / Calcium Free / CTLD / C-type Lectin-like Domain / Plasminogen kringle 4 binding / Tetranectin / Trans Proline
Function / homology
Function and homology information


kringle domain binding / platelet dense granule lumen / granular component / positive regulation of plasminogen activation / : / bone mineralization / cellular response to transforming growth factor beta stimulus / ossification / Platelet degranulation / heparin binding ...kringle domain binding / platelet dense granule lumen / granular component / positive regulation of plasminogen activation / : / bone mineralization / cellular response to transforming growth factor beta stimulus / ossification / Platelet degranulation / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / calcium ion binding / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing protocol with an explicit layer of water
AuthorsNielbo, S. / Thomsen, J.K. / Graversen, J.H. / Etzerodt, M. / Poulsen, F.M. / Thoegersen, H.C.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of the Plasminogen Kringle 4 Binding Calcium-Free Form of the C-Type Lectin-Like Domain of Tetranectin.
Authors: Nielbo, S. / Thomsen, J.K. / Graversen, J.H. / Jensen, P.H. / Etzerodt, M. / Poulsen, F.M. / Thoegersen, H.C.
History
DepositionNov 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetranectin


Theoretical massNumber of molelcules
Total (without water)13,0591
Polymers13,0591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Tetranectin / TN / Plasminogen-kringle 4 binding protein


Mass: 13059.368 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNA / Plasmid: pT7H6FXaTN3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P05452

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using standard spectra from the Varian Protein NMR pack.

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Sample preparation

DetailsContents: 0.6 mM U-15N-13C;
Solvent system: 90% H20, 10% D20, 1 mM NaN3, 2 mM EDTA, pH 6.7
Sample conditionsIonic strength: 1 mM NaN3, 2 mM EDTA / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe1Delaglioprocessing
Pronto20020313Kjaerdata analysis
X-PLOR98.1Brungerdata analysis
CYANA1.0.6Guentertstructure solution
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing protocol with an explicit layer of water
Software ordinal: 1
Details: The structure is based on 1552 NOE-derived distance restraints and 194 Dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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