+Open data
-Basic information
Entry | Database: PDB / ID: 1zza | ||||||
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Title | Solution NMR Structure of the Membrane Protein Stannin | ||||||
Components | Stannin | ||||||
Keywords | MEMBRANE 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing, molecular dynamics | ||||||
Model type details | minimized average | ||||||
Authors | Buck-Koehntop, B.A. / Mascioni, A. / Buffy, J.J. / Veglia, G. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zza.cif.gz | 741.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zza.ent.gz | 631 KB | Display | PDB format |
PDBx/mmJSON format | 1zza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zza_validation.pdf.gz | 349.3 KB | Display | wwPDB validaton report |
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Full document | 1zza_full_validation.pdf.gz | 511.6 KB | Display | |
Data in XML | 1zza_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 1zza_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/1zza ftp://data.pdbj.org/pub/pdb/validation_reports/zz/1zza | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 3D 15N-separated NOESY |
NMR details | Text: 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 |
-Sample preparation
Details | Contents: 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 |
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Sample conditions | Ionic strength: 120 mM NaCl / pH: 4.0 / Pressure: ambient / Temperature: 333 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry simulated annealing, molecular dynamics Software ordinal: 1 Details: structures based on 468 NOE distance constraints, 70 distance restraints from hydrogen bonds | ||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 25 |