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- PDB-2n4f: EC-NMR Structure of Arabidopsis thaliana At2g32350 Determined by ... -

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Basic information

Entry
Database: PDB / ID: 2n4f
TitleEC-NMR Structure of Arabidopsis thaliana At2g32350 Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data. Northeast Structural Genomics Consortium target AR3433A
Componentsuncharacterized protein AR3433A
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha / beta / ubiquitin fold / EC-NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Protein Structure Initiative / PSI-Biology
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 / Uncharacterized protein At2g32350
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsTang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Methods / Year: 2015
Title: Protein structure determination by combining sparse NMR data with evolutionary couplings.
Authors: Tang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D.S. / Montelione, G.T.
History
DepositionJun 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 0THIS ENTRY 2N4F REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2KAN DETERMINED ...THIS ENTRY 2N4F REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2KAN DETERMINED BY AUTHORS: A.ELETSKY,J.L.MILLS,D.SUKUMARAN,J.HUA,R.SHASTRY,M.JIANG,C.CICCOSANTI,R.XIAO,J.LIU,J.K.EVERRET,G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE,T.SZYPERSKI,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: uncharacterized protein AR3433A


Theoretical massNumber of molelcules
Total (without water)11,0061
Polymers11,0061
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 / 100lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein uncharacterized protein AR3433A


Mass: 11005.522 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g32350 / Plasmid: pET 14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9ZV63, UniProt: F4ITP6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: AUTHOR USED THE EXPERIMENTAL DATA FROM ENTRY 2KAN.

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Processing

NMR software
NameDeveloperClassification
RosettaBaker, D.refinement
EVfold-plmdata analysis
ASDPdata analysis
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.data analysis
EC-NMRdata analysis
TALOS+data analysis
ReduceRichardson, J., Richardson, D.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Protons from the Rosetta models were removed and added back using Reduce.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 20

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