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- PDB-4aai: THERMOSTABLE PROTEIN FROM HYPERTHERMOPHILIC VIRUS SSV-RH -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4aai
TitleTHERMOSTABLE PROTEIN FROM HYPERTHERMOPHILIC VIRUS SSV-RH
ComponentsORF E73
KeywordsVIRAL PROTEIN / EXTREMOPHILE / ARCHAEA / RIBBON-HELIX-HELIX PROTEINS / DNA-BINDING PROTEINS
Function / homologyArc Repressor Mutant - #150 / Arc Repressor Mutant / Orthogonal Bundle / Mainly Alpha / ORF E73
Function and homology information
Biological speciesSULFOLOBUS VIRUS RAGGED HILLS
MethodSOLUTION NMR / ENERGY MINIMIZATION
AuthorsSchlenker, C. / Goel, A. / Tripet, B.P. / Menon, S. / Lawrence, C.M. / Copie, V.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Studies of E73 from a Hyperthermophilic Archaeal Virus Identify the "Rh3" Domain, an Elaborated Ribbon-Helix- Helix Motif Involved in DNA Recognition.
Authors: Schlenker, C. / Goel, A. / Tripet, B.P. / Menon, S. / Willi, T. / Dlakic, M. / Young, M.J. / Lawrence, C.M. / Copi, V.
History
DepositionDec 2, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionJan 11, 2012ID: 4A1Q
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2May 1, 2013Group: Atomic model / Other / Refinement description
Revision 1.3Feb 5, 2014Group: Atomic model / Other
Revision 1.4Dec 17, 2014Group: Other
Revision 1.5Nov 30, 2016Group: Atomic model / Other
Revision 1.6Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF E73
B: ORF E73


Theoretical massNumber of molelcules
Total (without water)17,2782
Polymers17,2782
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein ORF E73


Mass: 8639.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS VIRUS RAGGED HILLS
Description: ORF E73 OBTAINED FROM SULFOLOBUS SPINDLE SHAPED VIRUS (RAGGED HILLS) THAT ATTACKS THE CRENARCHAEA SULFOLOBUS SOLFATARCUS
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6TRU9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
2213D CBCA(CO)NH
3313D C(CO)NH
4413D H(CCO)NH
5512D 1H-13C HSQC
6613D HBHA(CO)NH
7713D (H)CCH-TOCSY
8812D 1H-15N HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED E73.

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Sample preparation

DetailsContents: PMSF 1 MM, SODIUM AZIDE 0.01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.05 5.0 1.0 atm312.0 K
20.05 5.0 1.0 atm312.0 K
30.05 5.0 1.0 atm312.0 K
40.05 5.0 1.0 atm312.0 K
50.05 5.0 1.0 atm312.0 K
60.05 5.0 1.0 atm312.0 K
70.05 5.0 1.0 atm312.0 K
80.05 5.0 1.0 atm312.0 K
90.05 5.0 1.0 atm312.0 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
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, READ,RICE,SIMONSON,WARRENrefinement
ARIAstructure solution
CNSstructure solution
RefinementMethod: ENERGY MINIMIZATION / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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