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- PDB-2jya: NMR solution structure of protein ATU1810 from Agrobacterium tume... -

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Basic information

Entry
Database: PDB / ID: 2jya
TitleNMR solution structure of protein ATU1810 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium target AtR23, Ontario Centre for Structural Proteomics Target ATC1776
ComponentsUncharacterized protein Atu1810
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein with unknown function ATU1810 / Ontario Centre for Structural Proteomics / OCSP / ATC1776 / AtR23 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H / : / electron transport chain
Similarity search - Function
atu1810 like domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsLemak, A. / Yee, A. / Gutmanas, A. / Fares, C. / Karra, M. / Semesi, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: Solution structure of protein ATU1810 form Agrobacterium tumefaciens.
Authors: Lemak, A. / Yee, A. / Gutmanas, A. / Fares, C. / Karra, M. / Semesi, A. / Arrowsmith, C.H.
History
DepositionDec 7, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Atu1810


Theoretical massNumber of molelcules
Total (without water)12,2211
Polymers12,2211
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein Atu1810 / AGR_C_3324p


Mass: 12220.831 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: Atu1810, AGR_C_3324 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UEE9, UniProt: A9CIL3*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
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D HNCO
1613D HNCA
1713D H(CCO)NH
1813D (H)C(CCO)NH
1923D (H)CCH-TOCSY
11023D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11412D 1H-15N HSQC(IPAP)
11513D TROSY-HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] Atu1810, 10 mM TRIS, 300 mM sodium chloride, 0.1 % sodium azide, 10 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] Atu1810, 10 mM TRIS, 300 mM sodium chloride, 0.1 % sodium azide, 10 mM benzamidine, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAtu1810[U-13C; U-15N]1
10 mMTris-HCl1
300 mMsodium chloride1
0.1 %sodium azide1
10 mMbenzamidine1
0.5 mMAtu1810[U-13C; U-15N]2
10 mMTris-HCl2
300 mMsodium chloride2
0.1 %sodium azide2
10 mMbenzamidine2
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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