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- PDB-2kyz: NMR structure of heavy metal binding protein TM0320 from Thermoto... -

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Basic information

Entry
Database: PDB / ID: 2kyz
TitleNMR structure of heavy metal binding protein TM0320 from Thermotoga maritima
ComponentsHeavy metal binding protein
KeywordsMETAL BINDING PROTEIN / Heavy metal binding protein / Thermotoga maritima / Structural Genomics / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / PSI
Function / homology
Function and homology information


metal ion transport / metal ion binding
Similarity search - Function
Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heavy metal binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsJaudzems, K. / Wahab, A. / Serrano, P. / Geralt, M. / Wuthrich, K. / Wilson, I.A. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of heavy metal binding protein TM0320 from Thermotoga maritima
Authors: Jaudzems, K. / Wahab, A. / Serrano, P. / Geralt, M. / Wuthrich, K. / Wilson, I.A.
History
DepositionJun 9, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Structure summary
Revision 1.3Aug 10, 2011Group: Derived calculations
Revision 1.4Mar 20, 2013Group: Other
Revision 1.5May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heavy metal binding protein


Theoretical massNumber of molelcules
Total (without water)7,8631
Polymers7,8631
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Heavy metal binding protein


Mass: 7863.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0320 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9WYF6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: reduced form
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C(ali) NOESY
1313D 1H-13C(aro) NOESY
1414D APSY-HACANH
1515D APSY-(HA)CA(CO)NH
1615D APSY-CBCA(CO)NH
1712D 1H-15N HSQC
1812D 1H-13C HSQC

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Sample preparation

DetailsContents: 1.5 mM [U-98% 13C; U-98% 15N] TM0320, 20 mM sodium phosphate, 50 mM sodium chloride, 3 mM DTT, 0.03 % sodium azide, 95% H2O/5% D2O. Reduced form of the protein. The absence of bound metals ...Contents: 1.5 mM [U-98% 13C; U-98% 15N] TM0320, 20 mM sodium phosphate, 50 mM sodium chloride, 3 mM DTT, 0.03 % sodium azide, 95% H2O/5% D2O. Reduced form of the protein. The absence of bound metals was checked by adding 5mM EDTA, which did not cause any significant chemical shift perturbations.
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMTM0320-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
3 mMDTT-41
5 %D2O-51
0.03 %sodium azide-61
Sample conditionsIonic strength: 83.6 / pH: 6.0 / Pressure: AMBIENT / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
OPALp1.2Luginbuhl, Guntert, Billeter and Wuthrichrefinement
MOLMOL2K.1Koradi, Billeter and Wuthrichdata analysis
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
UNIO1.0.4Herrmann, T., Guntert, P., Wuthrich, K.structure solution
UNIO1.0.4Herrmann, T., Guntert, P., Wuthrich, K.peak picking
CARA1.8.4Keller, R.chemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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