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- PDB-2kd0: NMR solution structure of O64736 protein from Arabidopsis thalian... -

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Basic information

Entry
Database: PDB / ID: 2kd0
TitleNMR solution structure of O64736 protein from Arabidopsis thaliana. Northeast Structural Genomics Consortium MEGA Target AR3445A
ComponentsLRR repeats and ubiquitin-like domain-containing protein At2g30105
KeywordsSIGNALING PROTEIN / Ubiquitin-like protein / NESG / AR3445A / Leucine-rich repeat / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


signal transduction
Similarity search - Function
: / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...: / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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
LRR repeats and ubiquitin-like domain-containing protein At2g30105
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSwapna, G.V.T. / Shastry, R. / Foote, E. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y. / Acton, T.B. ...Swapna, G.V.T. / Shastry, R. / Foote, E. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of O64736 protein from Arabidopsis thaliana
Authors: Swapna, G.V.T. / Shastry, R. / Foote, E. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Nair, R. / Everett, J. / Huang, Y. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionDec 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 1.3Jun 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: LRR repeats and ubiquitin-like domain-containing protein At2g30105


Theoretical massNumber of molelcules
Total (without water)9,1971
Polymers9,1971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein LRR repeats and ubiquitin-like domain-containing protein At2g30105


Mass: 9196.788 Da / Num. of mol.: 1 / Fragment: UNP residues 11-85
Source method: isolated from a genetically manipulated source
Details: The first 10 residues of the sequence MGHHHHHHSH correspond to a N-terminal tag.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g30105, T27E13.16 / Plasmid: pET14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P0C895

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: O64736_ARATH protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D HNCO
1713D HBHANH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY
21122D 1H-15N HSQC
21222D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM [U-100% 13C; U-100% 15N] sample_1-1, 90% H2O/10% D2O90% H2O/10% D2O
21.80 mM [U-10% 13C; U-100% 15N] sample_2-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.8 mMsample_1-1[U-100% 13C; U-100% 15N]1
1.80 mMsample_2-2[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: 5mM CaCl2, 200mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AUTOASSIGN and the side chain assignments were completed ...Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AUTOASSIGN and the side chain assignments were completed manually. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-2.1. Dihedral angle constraints were obtained from TALOS. Completeness of assignments excluding the N-terminal tag-MGHHHHHHSH: backbone 100%, sidechain (aliphatic) 99%, sidechain (aromatic) 90%; stereospecific methyl assignments 100%. The assignments were validated using AVS software. Final structure quality factors were determined using PSVS-1.3; Ordered residues were defined as 12-19,22-82. RMSD (ordered residues) all backbone atoms: 0.5A, all heavy atoms: 0.8A. Ramachandran statistics for all ordered residues: most favoured 84.3%, additionally allowed 15.7%. Molprobity clashscore (raw/z-): 16.88/-1.37. Procheck scores for ordered residues: phi-psi, -0.50/-1.65, all, -0.19/-1.12
NMR constraintsNOE constraints total: 1287 / NOE intraresidue total count: 312 / NOE long range total count: 385 / NOE medium range total count: 229 / NOE sequential total count: 361
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.15 Å

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