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- PDB-2nnz: Solution structure of the hypothetical protein AF2241 from Archae... -

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Basic information

Entry
Database: PDB / ID: 2nnz
TitleSolution structure of the hypothetical protein AF2241 from Archaeoglobus fulgidus
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-barrel / Ontario Centre for Structural Proteomics / OCSP
Function / homologyTM1367-like / Cyclophilin TM1367-like domain / Cyclophilin-like / Cyclophilin - #20 / Cyclophilin / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta / Cyclophil_like domain-containing protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsAi, X. / Semesib, A. / Yee, A. / Arrowsmith, C.H. / Li, S.S.C. / Choy, W.Y. / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: J.Biomol.Nmr / Year: 2007
Title: Hypothetical protein AF2241 from Archaeoglobus fulgidus adopts a cyclophilin-like fold.
Authors: Ai, X. / Li, L. / Semesi, A. / Yee, A. / Arrowsmith, C.H. / Li, S.S. / Choy, W.Y.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 5, 2020Group: Database references / Other / Category: database_2 / pdbx_database_status / Item: _pdbx_database_status.status_code_cs
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 15, 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: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)17,1351
Polymers17,1351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Hypothetical protein


Mass: 17135.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF2241 / Plasmid: pMgk / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(Gold DE3) / References: UniProt: O28042

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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: The structure was determined using standard 3D heteronuclear techniques

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Sample preparation

DetailsContents: 0.3mM AF2241 U-15N,13C, 10mM MOPS buffer, 450mM NaCl, 10uM Zn2+, 10mM DTT, 1mM benzamidine, 1x inhibitor mixture, 0.01% NaN3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 450 mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T. et al.structure solution
CNS1.1Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1463 restraints, 1313 are NOE-derived distance constraints and 150 are dihedral angle restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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