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- PDB-2hi6: Solution NMR structure of UPF0107 protein AF_0055, Northeast Stru... -

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Basic information

Entry
Database: PDB / ID: 2hi6
TitleSolution NMR structure of UPF0107 protein AF_0055, Northeast Structural Genomics Consortium Target GR101
ComponentsUPF0107 protein AF0055
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / UPF0107 protein AF_0055GFT / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyAconitase X swivel domain, putative / Aconitase X subunit 2, putative / Aconitase X subunit 2, archaeal, putative / Aconitase X swivel domain / Phosphohistidine domain / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta / UPF0107 protein AF_0055
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsLiu, G. / Atreya, H. / Xu, D. / Sukumaran, D.K. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Liu, G. / Atreya, H. / Xu, D. / Sukumaran, D.K. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of UPF0107 protein AF_0055, Northeast Structural Genomics Consortium Target GR101 (CASP Target)
Authors: Liu, G. / Atreya, H. / Xu, D. / Sukumaran, D.K. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / ...Authors: Liu, G. / Atreya, H. / Xu, D. / Sukumaran, D.K. / Chen, C.X. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: UPF0107 protein AF0055


Theoretical massNumber of molelcules
Total (without water)15,3791
Polymers15,3791
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein UPF0107 protein AF0055


Mass: 15378.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: GR101-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O30181

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111SIMULTANEOUS HETERONUCLEAR RESOLVED [1H,1H]-NOESY
121GFT (4,3)D HNNCABCA
131GFT (4,3)D CABCA(CO)NHN
141GFT (4,3)D HABCAB(CO)NHN
151GFT (4,3)D (H)CCH

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Sample preparation

DetailsContents: 5-5.5mM CaCl2, 100mM NaCl, 20mM NH4OAc, 10mM DTT, 0.02% NaN3, pH 5.5, 5% D2O, 95% H2O U-15N,13C
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1ccollection
NMRPipe2.3Delaglio, Fprocessing
AutoAssign1.15.1Moseley, H.data analysis
AutoStructure2HUANG, Y.J.data analysis
CYANA2.1GUNTERT, P.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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