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- PDB-2kk8: NMR Solution Structure of a Putative Uncharacterized Protein obta... -

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Basic information

Entry
Database: PDB / ID: 2kk8
TitleNMR Solution Structure of a Putative Uncharacterized Protein obtained from Arabidopsis thaliana: Northeast Structural Genomics Consortium target AR3449A
ComponentsUncharacterized protein AT4g05270
KeywordsStructural Genomics / Unknown function / Arabidopsis thaliana / AR3449A / uncharacterized putative protein / NESG / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


proteasome binding / polyubiquitin modification-dependent protein binding / ubiquitin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleoplasm / cytosol
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like superfamily protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMani, R. / Gurla, S.V.T. / Shastry, R. / Ciccosanti, C. / Foote, E. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y. ...Mani, R. / Gurla, S.V.T. / Shastry, R. / Ciccosanti, C. / Foote, E. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y. / Acton, T. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of a Putative Uncharacterized Protein obtained from Arabidopsis thaliana: Northeast Structural Genomics Consortium Target AR3449A
Authors: Mani, R. / Gurla, S.V.T. / Shastry, R. / Ciccosanti, C. / Foote, E. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y. / Acton, T. / Rost, B. / Montelione, G.T.
History
DepositionJun 16, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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 8, 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: Uncharacterized protein AT4g05270


Theoretical massNumber of molelcules
Total (without water)9,6791
Polymers9,6791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 AT4g05270


Mass: 9679.011 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g05270 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9M0W8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C aliphatic NOESY
1313D 1H-13C aromatic NOESY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1612D 1H-15N HSQC
1712D 1H-13C HSQC
1813D HBHA(CO)NH
1913D CBCA(CO)NH
1101(4,3)D GFT-HNNCABCA
1111(4,3)D GFT-CABCA(CO)NHN
11213D HNCO
11313D HNCA
11413D HN(CA)CB
11513D H(CCO)NH
11613D (H)CCH-TOCSY
11723D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11.11 mM [U-100% 13C; U-100% 15N] AR3449A, 90% H2O/10% D2O90% H2O/10% D2O
21.22 mM [U-10% 13C; U-100% 15N] AR3449A, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.11 mMAR3449A-1[U-100% 13C; U-100% 15N]1
1.22 mMAR3449A-2[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: 5mM CaCl2, 10mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was obtained using triple resonance NMR spectroscopy. GFT-NMR experiments were used for backbone assignments. Automated NOESY assignments were made using AUTOSTRUCTURE and ...Details: The structure was obtained using triple resonance NMR spectroscopy. GFT-NMR experiments were used for backbone assignments. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-2.1. Dihedral angle constraints were obteined from TALOS. The assignments were validated using AVS software. FInal structure factors determined using PSVS: ordered residues: alpha helices- 33.44, 67-70, beta strands- 22-27, 11-17, 78-82, 51-55, 58-59. Ramachandran statistics for ordered residues: 89.1% most favoured regions, 10.9% additionally favoured regions. Procheck scores for ordered residues (RAW/Z): phi/psi -0.43/-1.38, all -0.18/-1.06, MolProbity clashscores- 21.46/-2.16. RPF score for goodness fit to the NOESY data: Recall-0.998, Precision-0.93, final dp-score-0.869
NMR constraintsNOE constraints total: 1362 / NOE intraresidue total count: 237 / NOE long range total count: 454 / NOE medium range total count: 317 / NOE sequential total count: 354 / Protein phi angle constraints total count: 91 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.01 Å / Maximum upper distance constraint violation: 0.2 Å

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