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- PDB-1t0g: Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a ... -

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Basic information

Entry
Database: PDB / ID: 1t0g
TitleHypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome b5 like fold
Componentscytochrome b5 domain-containing protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / At2g24940.1 / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


vacuole / steroid binding / nucleus / cytosol
Similarity search - Function
Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Roll / Alpha Beta
Similarity search - Domain/homology
Probable steroid-binding protein 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / molecular dynamics, torsion angle dynamics
AuthorsSong, J. / Vinarov, D.A. / Tyler, E.M. / Shahan, M.N. / Tyler, R.C. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biomol.NMR / Year: 2004
Title: Hypothetical protein At2g24940.1 from Arabidopsis thaliana has a cytochrome b5 like fold
Authors: Song, J. / Vinarov, D.A. / Tyler, E.M. / Shahan, M.N. / Tyler, R.C. / Markley, J.L.
History
DepositionApr 8, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionApr 13, 2004ID: 1SV7
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytochrome b5 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)12,1711
Polymers12,1711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100back calculated data agree with experimental NOESY spectrum,target function
RepresentativeModel #1closest to the average

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Components

#1: Protein cytochrome b5 domain-containing protein


Mass: 12171.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: At2g24940.1 / Plasmid: PEU(N)HIS6 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9SK39

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: This structure was determined using standard 3D heteronuclear NMR techniques

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Sample preparation

DetailsContents: 0.5 mM At2g24940.1; 50mM KCl; 10 mM KH2PO4; 0.02% (w/v) sodium azide; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.2Brukercollection
NMRPipe2.1Delaglio et alprocessing
Sparky3.72Goddard and Knellerdata analysis
CYANA1.0.5Gunter et alstructure solution
XPLOR-NIH2.9.3Brunger et al; Schwieters et alrefinement
RefinementMethod: molecular dynamics, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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