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- PDB-2rog: Solution structure of Thermus thermophilus HB8 TTHA1718 protein i... -

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Basic information

Entry
Database: PDB / ID: 2rog
TitleSolution structure of Thermus thermophilus HB8 TTHA1718 protein in living E. coli cells
ComponentsHeavy metal binding protein
KeywordsMETAL BINDING PROTEIN / protein
Function / homology
Function and homology information


Heavy metal binding protein HIPP/ATX1-like / 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 speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSakakibara, D. / Sasaki, A. / Ikeya, T. / Hamatsu, J. / Koyama, H. / Mishima, M. / Mikawa, T. / Waelchli, M. / Smith, B.O. / Shirakawa, M. ...Sakakibara, D. / Sasaki, A. / Ikeya, T. / Hamatsu, J. / Koyama, H. / Mishima, M. / Mikawa, T. / Waelchli, M. / Smith, B.O. / Shirakawa, M. / Guentert, P. / Ito, Y.
CitationJournal: Nature / Year: 2009
Title: Protein structure determination in living cells by in-cell NMR spectroscopy
Authors: Sakakibara, D. / Sasaki, A. / Ikeya, T. / Hamatsu, J. / Hanashima, T. / Mishima, M. / Yoshimasu, M. / Hayashi, N. / Mikawa, T. / Walchli, M. / Smith, B.O. / Shirakawa, M. / Guntert, P. / Ito, Y.
History
DepositionMar 21, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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)7,0511
Polymers7,0511
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Heavy metal binding protein / TTHA1718 Heavy metal binding protein


Mass: 7051.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHL2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D CBCANH
1513D HNCO
1613D HN(CA)CO
1713D H(CCCO)NH
1813D CC(CO)NH
1913D (H)CCH-TOCSY
11014D HCC(CO)NH
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

DetailsContents: 3-4 mM [U-13C; U-15N] TTHA1718 heavy metal binding protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 3 mM / Component: TTHA1718 heavy metal binding protein / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 / pH: 7.5 / Pressure: AMBIENT / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
Azara2.7Boucherprocessing
Azara2.7Boucherpeak picking
ANSIGKraulischemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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