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- PDB-1zza: Solution NMR Structure of the Membrane Protein Stannin -

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Basic information

Entry
Database: PDB / ID: 1zza
TitleSolution NMR Structure of the Membrane Protein Stannin
ComponentsStannin
KeywordsMEMBRANE PROTEIN / helix
Function / homology
Function and homology information


response to toxic substance / mitochondrial outer membrane / membrane => GO:0016020 / metal ion binding / cytoplasm
Similarity search - Function
membrane protein stannin / Stannin transmembrane / Stannin unstructured linker / Stannin cytoplasmic / Stannin superfamily / Stannin / Stannin transmembrane / Stannin unstructured linker / Stannin cytoplasmic / MYOD Basic-Helix-Loop-Helix Domain, subunit B ...membrane protein stannin / Stannin transmembrane / Stannin unstructured linker / Stannin cytoplasmic / Stannin superfamily / Stannin / Stannin transmembrane / Stannin unstructured linker / Stannin cytoplasmic / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsBuck-Koehntop, B.A. / Mascioni, A. / Buffy, J.J. / Veglia, G.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure, dynamics, and membrane topology of stannin: a mediator of neuronal cell apoptosis induced by trimethyltin chloride.
Authors: Buck-Koehntop, B.A. / Mascioni, A. / Buffy, J.J. / Veglia, G.
History
DepositionJun 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stannin


Theoretical massNumber of molelcules
Total (without water)9,6501
Polymers9,6501
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)25 / 100structures with the lowest energy
RepresentativeModel #22minimized average structure

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Components

#1: Protein Stannin / / AG8_1


Mass: 9650.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNN / Plasmid: pMal-c2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75324

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N-separated NOESY
NMR detailsText: Backbone assignments were made using 3D-TROSY based HNCA, HN(CO)CA, HNCACB, CBCA(CO)NH and HNCO experiments. Side chains and NOEs were assigned with 3D [1H, 15N]-TOCSY-HSQC and 3D [1H,15N]-NOESY-HSQC experiments

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Sample preparation

DetailsContents: 0.5-0.7 mM Stannin U-15N or U-15N/13C; 20 mM phosphate buffer; 600 mM d25-sodium dodecyl sulfate; 90% H2O; 10% D2O; 0.02% sodium azide; 0.7 mM DTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 mM NaCl / pH: 4.0 / Pressure: ambient / Temperature: 333 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe97.027.12.56Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.111Goddard and Knellerdata analysis
X-PLOR2.11Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR2.11Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: structures based on 468 NOE distance constraints, 70 distance restraints from hydrogen bonds
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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