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- PDB-1m31: Three-Dimensional Solution Structure of Apo-Mts1 -

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Basic information

Entry
Database: PDB / ID: 1m31
TitleThree-Dimensional Solution Structure of Apo-Mts1
ComponentsPlacental calcium-binding protein
KeywordsMETAL BINDING PROTEIN / NON-COVALENT HOMODIMER / X-TYPE FOUR-HELIX BUNDLE
Function / homology
Function and homology information


RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / perinuclear region of cytoplasm ...RAGE receptor binding / chemoattractant activity / transition metal ion binding / epithelial to mesenchymal transition / calcium-dependent protein binding / actin binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / calcium ion binding / perinuclear region of cytoplasm / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...S-100 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance Geometry, Simulated Annealing
AuthorsVallely, K.M. / Rustandi, R.R. / Ellis, K.C. / Varlamova, O. / Bresnick, A.R. / Weber, D.J.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structure of human Mts1 (S100A4) as determined by NMR spectroscopy.
Authors: Vallely, K.M. / Rustandi, R.R. / Ellis, K.C. / Varlamova, O. / Bresnick, A.R. / Weber, D.J.
History
DepositionJun 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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: Placental calcium-binding protein
B: Placental calcium-binding protein


Theoretical massNumber of molelcules
Total (without water)23,4912
Polymers23,4912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 75structures with the least restraint violations
RepresentativeModel #8lowest energy

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Components

#1: Protein Placental calcium-binding protein / Calvasculin / S100 calcium-binding protein A4 / MTS1 protein


Mass: 11745.538 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26447

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1312D 1H-15N HSQC
1413D 15N separated HOHAHA
1514D 13C-separated NOESY
1613D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM Mts1, U-15N, 16mM D11-Tris, 2mM EGTA, 0.3mM NAN3, 8mM NaCl, 6mM DTT93% H2O/7% D2O
23mM Mts1, U-13C,15N, 16mM D11-Tris, 2mM EGTA, 0.3mM NAN3, 8mM NaCl, 6mM DTT93% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125mM 6.5 ambient 310 K
225mM 6.5 ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe1.8Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., and Bax, A.processing
X-PLOR3.851Brunger, A.T.structure solution
X-PLOR3.851Brunger, A.T.refinement
RefinementMethod: Distance Geometry, Simulated Annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 75 / Conformers submitted total number: 20

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