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- PDB-2i9y: Solution structure of Arabidopsis thaliana protein At1g70830, a m... -

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Basic information

Entry
Database: PDB / ID: 2i9y
TitleSolution structure of Arabidopsis thaliana protein At1g70830, a member of the major latex protein family
Componentsmajor latex protein-like protein 28 or MLP-like protein 28
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / At1g70830 / Bet v1-like / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


defense response / mitochondrion / cytosol
Similarity search - Function
Pathogenesis-related protein Bet v I family / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / de la Cruz, N.B. / Lytle, B.L. / Peterson, F.C. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2009
Title: Structures of two Arabidopsis thaliana major latex proteins represent novel helix-grip folds.
Authors: Lytle, B.L. / Song, J. / de la Cruz, N.B. / Peterson, F.C. / Johnson, K.A. / Bingman, C.A. / Phillips, G.N. / Volkman, B.F.
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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: major latex protein-like protein 28 or MLP-like protein 28


Theoretical massNumber of molelcules
Total (without water)18,6821
Polymers18,6821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein major latex protein-like protein 28 or MLP-like protein 28


Mass: 18681.982 Da / Num. of mol.: 1 / Fragment: residues 17-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: AT1G70830, MLP28 / Plasmid: pEU-HIS / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9SSK9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING A CRYOGENIC PROBE.

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Sample preparation

DetailsContents: 0.7 mM At1g70830 U-15N/13C protein, 10 mM deuterated bis-tris, 5 mM Dithiothreitol, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.002 mM / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2004Delagio,F. et al.processing
XEASY1.3Eccles, C.; Guntert, P.; Billeter, M.; Wuthrich, K.data analysis
SPSCAN1.1.0R.W. Glaserdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structure solution
Xplor-NIH2.9.3SCHWIETERS, C.D., KUSZEWSKI, J.J., TJANDRA, N., CLORE, G.M.refinement
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1766 NOE CONSTRAINTS ( 597 INTRA, 423 SEQUENTIAL, 224 MEDIUM and 522 LONG RANGE CONSTRAINTS) AND 197 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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