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- PDB-2enk: Solution structure of a putativ DNA-binding domain of the humanso... -

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Basic information

Entry
Database: PDB / ID: 2enk
TitleSolution structure of a putativ DNA-binding domain of the humansolute carrier family 30 (zinc transporter) protein
ComponentsSolute carrier family 30 member 9
KeywordsSIGNALING PROTEIN / cation transporter / cobalt / zinc / cadmium / protein of unknown function duf993 / embryonic lung protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


zinc ion transport / intracellular zinc ion homeostasis / monoatomic cation transmembrane transporter activity / nuclear receptor coactivator activity / nuclear receptor binding / nucleotide-excision repair / cytoplasmic vesicle / membrane => GO:0016020 / cytoskeleton / chromatin binding ...zinc ion transport / intracellular zinc ion homeostasis / monoatomic cation transmembrane transporter activity / nuclear receptor coactivator activity / nuclear receptor binding / nucleotide-excision repair / cytoplasmic vesicle / membrane => GO:0016020 / cytoskeleton / chromatin binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Zinc transporter 9 / XPA domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A.K. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of a putativ DNA-binding domain of the humansolute carrier family 30 (zinc transporter) protein
Authors: Goroncy, A.K. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionMar 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Solute carrier family 30 member 9


Theoretical massNumber of molelcules
Total (without water)11,9211
Polymers11,9211
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Solute carrier family 30 member 9 / HUEL


Mass: 11921.370 Da / Num. of mol.: 1 / Fragment: putativ dna bind 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: SLC30A9 / Plasmid: P060313-04 / References: UniProt: Q6PML9

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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

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Sample preparation

DetailsContents: 0.34 mM PUTATIV_DNA_BIND_1 DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: AMBIENT / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.2P.GUNTERT ET AL.refinement
CYANA2.2.2P.GUNTERT ET AL.structure solution
XwinNMR3.5BRUKERcollection
NMRPipe20060702FRANK DELAGLIOprocessing
NMRView5.0.4BRUCE A. JOHNSONdata analysis
KUJIRA0.9821NAOHIRO KOBAYASHIdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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