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- PDB-2jmb: Solution structure of the protein Atu4866 from Agrobacterium tume... -

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Basic information

Entry
Database: PDB / ID: 2jmb
TitleSolution structure of the protein Atu4866 from Agrobacterium tumefaciens
ComponentsHypothetical protein Atu4866
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ontario Centre for Structural Proteomics / OCSP
Function / homologyUncharacterised protein family Atu4866 / Uncharacterised protein family Atu4866 / Atu4866-like superfamily / Agrobacterium tumefaciens protein Atu4866 / Lipocalin / Beta Barrel / Mainly Beta / Uncharacterized protein / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsAi, X. / Semesi, A. / Yee, A. / Arrowsmith, C.H. / Li, S.S.C. / Choy, W. / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: Solution structure of the protein Atu4866 from Agrobacterium tumefaciens
Authors: Ai, X. / Semesi, A. / Yee, A. / Arrowsmith, C.H. / Li, S.S.C. / Choy, W.
History
DepositionNov 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein Atu4866


Theoretical massNumber of molelcules
Total (without water)9,1641
Polymers9,1641
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 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Hypothetical protein Atu4866 / AGR_L_42p


Mass: 9164.038 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: Atu4866 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U6E1, UniProt: A9CH91*PLUS

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

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Sample preparation

DetailsContents: 0.4 mM [U-13C, U-15N] Atu4866, 10 mM sodium acetate, 300 mM NaCl, 10 uM Zn2+, 10 mM DTT, 0.01% NaN3, 1x v/v inhibitor mixture, 10 mM benzamidine, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: Atu4866 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0.45 / pH: 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
NMRView5.2.2Johnsondata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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