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- PDB-2kjg: Solution structure of an archaeal protein SSO6904 from hypertherm... -

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Basic information

Entry
Database: PDB / ID: 2kjg
TitleSolution structure of an archaeal protein SSO6904 from hyperthermophilic Sulfolobus solfataricus
ComponentsArchaeal protein SSO6904
KeywordsMETAL BINDING PROTEIN / hypothetical protein / helical protein
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #970 / Calcium binding protein SSO6904 / Calcium binding protein SSO6904 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Ca_bind_SSO6904 domain-containing protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsFeng, Y. / Yao, H. / Wang, J.
CitationJournal: Proteins / Year: 2009
Title: Solution structure and calcium binding of protein SSO6904 from the hyperthermophilic archaeon Sulfolobus solfataricus.
Authors: Feng, Y. / Yao, H. / Wang, J.
History
DepositionMay 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaeal protein SSO6904


Theoretical massNumber of molelcules
Total (without water)11,9141
Polymers11,9141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Archaeal protein SSO6904


Mass: 11913.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO6904 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE1

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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 HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1713D HN(CA)CO
1813D HBHA(CO)NH
1913D HBHANH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY-HSQC
11213D 1H-13C NOESY-HSQC

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Sample preparation

DetailsContents: 1-1.5 mM [U-13C; U-15N] SS6904, 50 mM potassium phosphate, 100 mM potassium chloride, 10% v/v [U-99.8% 2H] D2O, 0.02% w/v DSS, 0.02% w/v sodium azide, 50 mM arginine, 50 mM glutamic acid, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSS6904-1[U-13C; U-15N]1-1.51
50 mMpotassium phosphate-21
100 mMpotassium chloride-31
10 v/vD2O-4[U-99.8% 2H]1
0.02 w/vDSS-51
0.02 w/vsodium azide-61
50 mMarginine-71
50 mMglutamic acid-81
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.peak picking
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.data analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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