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- PDB-2tmp: N-TERMINAL DOMAIN OF TISSUE INHIBITOR OF METALLOPROTEINASE-2 (N-T... -

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Entry
Database: PDB / ID: 2tmp
TitleN-TERMINAL DOMAIN OF TISSUE INHIBITOR OF METALLOPROTEINASE-2 (N-TIMP-2), NMR, 49 STRUCTURES
ComponentsTISSUE INHIBITOR OF METALLOPROTEINASES-2
KeywordsMETALLOPROTEASE INHIBITOR / TIMP / METALLOPROTEINASE INHIBITOR / OB PROTEIN FOLD
Function / homology
Function and homology information


negative regulation of metallopeptidase activity / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / peptidase inhibitor activity / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / response to hormone / response to cytokine / extracellular matrix ...negative regulation of metallopeptidase activity / negative regulation of membrane protein ectodomain proteolysis / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / peptidase inhibitor activity / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / response to hormone / response to cytokine / extracellular matrix / specific granule lumen / tertiary granule lumen / : / protease binding / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold ...Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Metalloproteinase inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING USING TORSION ANGLE DYNAMICS
AuthorsMuskett, F.W. / Frenkiel, T.A. / Feeney, J. / Freedman, R.B. / Carr, M.D. / Williamson, R.A.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: High resolution structure of the N-terminal domain of tissue inhibitor of metalloproteinases-2 and characterization of its interaction site with matrix metalloproteinase-3.
Authors: Muskett, F.W. / Frenkiel, T.A. / Feeney, J. / Freedman, R.B. / Carr, M.D. / Williamson, R.A.
#1: Journal: Biochemistry / Year: 1997
Title: Mapping the Binding Site for Matrix Metalloproteinase on the N-Terminal Domain of the Tissue Inhibitor of Metalloproteinases-2 by NMR Chemical Shift Perturbation
Authors: Williamson, R.A. / Carr, M.D. / Frenkiel, T.A. / Feeney, J. / Freedman, R.B.
#2: Journal: Eur.J.Biochem. / Year: 1996
Title: Chemically and Conformationally Authentic Active Domain of Human Tissue Inhibitor of Metalloproteinases-2 Refolded from Bacterial Inclusion Bodies
Authors: Williamson, R.A. / Natalia, D. / Gee, C.K. / Murphy, G. / Carr, M.D. / Freedman, R.B.
#3: Journal: Biochemistry / Year: 1994
Title: Solution Structure of the Active Domain of Tissue Inhibitor of Metalloproteinases-2. A New Member of the Ob Fold Protein Family
Authors: Williamson, R.A. / Martorell, G. / Carr, M.D. / Murphy, G. / Docherty, A.J. / Freedman, R.B. / Feeney, J.
#4: Journal: Biochem.J. / Year: 1990
Title: Disulphide Bond Assignment in Human Tissue Inhibitor of Metalloproteinases (Timp)
Authors: Williamson, R.A. / Marston, F.A. / Angal, S. / Koklitis, P. / Panico, M. / Morris, H.R. / Carne, A.F. / Smith, B.J. / Harris, T.J. / Freedman, R.B.
History
DepositionMay 26, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TISSUE INHIBITOR OF METALLOPROTEINASES-2


Theoretical massNumber of molelcules
Total (without water)14,1091
Polymers14,1091
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)49 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #3

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Components

#1: Protein TISSUE INHIBITOR OF METALLOPROTEINASES-2 / METALLOPROTEINASE INHIBITOR / TIMP-2


Mass: 14109.167 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-127 / Mutation: A21T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN REFOLDED FROM INCLUSION BODIES / Plasmid: PET23D / Species (production host): Escherichia coli
Cellular location (production host): INTRACELLULAR INCLUSION BODIES
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P16035
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
1212D-TOCSY
1312D-COSY
1413D-NOESY-TOCSY
1512D-HSQC
1613D-15N-NOESY-HSQC
1713D-15N-HNHA
1813D-15N-HNHB
1913D (H)CCH-TOCSY
11013D CBCA(CO)NH
11113D-CBCAHN
11213D-13C-HMQC-NOESY
NMR detailsText: THE STRUCTURE CLOSEST TO THE MEAN OF THE 49 CONFORMERS

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Sample preparation

DetailsContents: AQUEOUS
Sample conditionsIonic strength: 125 mM / pH: 6.7 / Pressure: 1 ATMOSPHERE / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS & INOVA / Manufacturer: Varian / Model: UNITYPLUS & INOVA / Field strength: 600 MHz

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Processing

Software
NameClassification
DYANAmodel building
DYANArefinement
NMR software
NameVersionDeveloperClassification
DYANA1.4GUNTERT,WUTHRICHrefinement
DYANAstructure solution
RefinementMethod: SIMULATED ANNEALING USING TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: SEE GUNTERT ET AL. (1997) J. MOL. BIOL. 273(1), 283-298
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 49

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