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- PDB-2jq4: Complete resonance assignments and solution structure calculation... -

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Basic information

Entry
Database: PDB / ID: 2jq4
TitleComplete resonance assignments and solution structure calculation of ATC2521 (NESG ID: AtT6) from Agrobacterium tumefaciens
ComponentsHypothetical protein Atu2571
KeywordsSTRUCTURAL GENOMICS / Agrobacterium tumefaciens / ATC2521 / unknown function / ATC / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Aminoacyl carrier protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsSrisailam, S. / Lemak, A. / Yee, A. / Karra, M.D. / Lukin, J.A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Solution Structure of a protein (ATC2521)of unknown function from Agrobacterium tumefaciens
Authors: Srisailam, S. / Lemak, A. / Yee, A. / Karra, M.D. / Lukin, J.A. / Arrowsmith, C.H.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Database references
Revision 1.4Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Dec 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
Revision 1.6May 8, 2024Group: Database references / Category: 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 Atu2571


Theoretical massNumber of molelcules
Total (without water)11,5641
Polymers11,5641
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 Hypothetical protein Atu2571 / AGR_C_4658p


Mass: 11563.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: strain C58 / ATCC 33970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UCC7, UniProt: A9CHM9*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 HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11123D (H)CCH-TOCSY
11223D 1H-13C NOESY
11322D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] ATC2521, 10 mM TRIS, 5 % glycerol, 1 mM Benzamidine, 300 mM sodium chloride, 0.01 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] ATC2521, 10 mM TRIS, 5 % glycerol, 1 mM Benzamidine, 300 mM sodium chloride, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMATC2521[U-100% 13C; U-100% 15N]1
10 mMTRIS1
5 %glycerol1
1 mMBenzamidine1
300 mMsodium chloride1
0.01 %sodium azide1
1 mMATC2521[U-100% 13C; U-100% 15N]2
10 mMTRIS2
5 %glycerol2
1 mMBenzamidine2
300 mMsodium chloride2
0.01 %sodium azide2
Sample conditionsIonic strength: 0.3 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / 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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