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- PDB-2jz4: Putative 32 kDa myrosinase binding protein At3g16450.1 from Arabi... -

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Basic information

Entry
Database: PDB / ID: 2jz4
TitlePutative 32 kDa myrosinase binding protein At3g16450.1 from Arabidopsis thaliana
ComponentsJasmonate inducible protein isolog
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / myrosinase binding protein / At3g16450.1 / SAIL / stereo-array isotope labeling / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


plasmodesma / response to zinc ion / response to cold / carbohydrate binding / nucleus
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Jacalin-related lectin 33
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTakeda, N. / Sugimori, N. / Torizawa, T. / Terauchi, T. / Ono, A.M. / Yagi, H. / Yamaguchi, Y. / Kato, K. / Ikeya, T. / Guntert, P. ...Takeda, N. / Sugimori, N. / Torizawa, T. / Terauchi, T. / Ono, A.M. / Yagi, H. / Yamaguchi, Y. / Kato, K. / Ikeya, T. / Guntert, P. / Aceti, D.J. / Markley, J.L. / Kainosho, M. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: Febs J. / Year: 2008
Title: Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR.
Authors: Takeda, M. / Sugimori, N. / Torizawa, T. / Terauchi, T. / Ono, A.M. / Yagi, H. / Yamaguchi, Y. / Kato, K. / Ikeya, T. / Jee, J. / Guntert, P. / Aceti, D.J. / Markley, J.L. / Kainosho, M.
#1: Journal: J.Biomol.NMR / Year: 2004
Title: 1H, 13C and 15N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana, At3g16450.1
Authors: Sugimori, N. / Torizawa, T. / Aceti, D.J. / Thao, S. / Markley, J.L. / Kainosho, M.
History
DepositionDec 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: 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: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: Jasmonate inducible protein isolog


Theoretical massNumber of molelcules
Total (without water)31,9281
Polymers31,9281
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Jasmonate inducible protein isolog / At3g16450/MDC8_8 / Jasmonate inducible protein / myrosinase binding protein-like


Mass: 31928.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: Cell-free protein synthesis / Gene: At3g16450.1, T02O04.5 / Plasmid: pIVEX2.3d / Production host: Escherichia coli (E. coli) / References: UniProt: O04311

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D HNCA
1613D HNCO
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D HN(CA)CB
11013D HN(CO)CA
11113D CBCA(CO)NH
11213D H(CCO)NH

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Sample preparation

DetailsContents: 0.2 mM stereo-array isotope labeling (SAIL) At3g16450.1, 100 mM potassium chloride, 20 mM [U-99% 2H] bis-TRIS-d19, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMAt3g16450.1stereo-array isotope labeling (SAIL)1
100 mMpotassium chloride1
20 mMbis-TRIS-d19[U-99% 2H]1
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: Ambient / Temperature: 300.6 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGoddardchemical shift assignment
OPALp1.4(OPALP) Koradi, Billeter, Guntertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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