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- PDB-2kck: NMR solution structure of the Northeast Structural Genomics Conso... -

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Entry
Database: PDB / ID: 2kck
TitleNMR solution structure of the Northeast Structural Genomics Consortium (NESG) target MrR121A
ComponentsTPR repeat
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Tetratricopeptide repeat / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily ...: / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMethanococcus maripaludis (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBarb, A.W. / Lee, H.-W. / Wang, X. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. ...Barb, A.W. / Lee, H.-W. / Wang, X. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the Northeast Structural Genomics Target MrR121A
Authors: Barb, A.W. / Lee, H.-W. / Wang, X. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H.
History
DepositionDec 22, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR repeat


Theoretical massNumber of molelcules
Total (without water)13,2881
Polymers13,2881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein TPR repeat


Mass: 13287.620 Da / Num. of mol.: 1 / Fragment: UNP residues 24-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: MMP1143 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6LY49
Sequence detailsTHE SEQUENCE DIFFERENCES ARISE FROM STRAIN VARIATIONS. THE ORGANISM AUTHORS USED FOR CLONING HAD A ...THE SEQUENCE DIFFERENCES ARISE FROM STRAIN VARIATIONS. THE ORGANISM AUTHORS USED FOR CLONING HAD A SLIGHTLY DIFFERENT GENOME THAN THE ORGANISM DESCRIBED IN THE SEQUENCE DATABASE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCO
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1612D 1H-15N HSQC
2712D 1H-15N HSQC
3812D 1H-15N HSQC
1912D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] MrR121A-1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: MrR121A-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
VnmrJVariancollection
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: First rounds of refinement with CYANA (ver 2), then XPLOR (ver 2.18) with RDC refinement
NMR constraintsNOE constraints total: 1218 / NOE intraresidue total count: 232 / NOE long range total count: 333 / NOE medium range total count: 368 / NOE sequential total count: 285 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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