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- PDB-2n4c: EC-NMR Structure of Agrobacterium tumefaciens Atu1203 Determined ... -

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Basic information

Entry
Database: PDB / ID: 2n4c
TitleEC-NMR Structure of Agrobacterium tumefaciens Atu1203 Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data. Northeast Structural Genomics Consortium target AtT10
ComponentsUncharacterized protein Atu1203
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative metal-binding domain ATU1203 / EC-NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Protein Structure Initiative / PSI-Biology / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HMA domain-containing protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
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) / Ontario Centre for Structural Proteomics (OCSP)
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 2N4C REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2K2P DETERMINED ...THIS ENTRY 2N4C REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2K2P DETERMINED BY AUTHORS: A.LEMAK,A.GUTMANAS,A.YEE,A.SEMESI,C.H.ARROWSMITH,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Atu1203


Theoretical massNumber of molelcules
Total (without water)8,7671
Polymers8,7671
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 Atu1203


Mass: 8766.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Strain: C58 / Gene: Atu1203 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CJD6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: AUTHOR USED THE EXPERIMENTAL DATA FROM ENTRY 2K2P.

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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: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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