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- PDB-1q53: SOLUTION STRUCTURE OF HYPOTHETICAL ARABIDOPSIS THALIANA PROTEIN A... -

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Basic information

Entry
Database: PDB / ID: 1q53
TitleSOLUTION STRUCTURE OF HYPOTHETICAL ARABIDOPSIS THALIANA PROTEIN AT3G17210. CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS TARGET 13081
Componentsexpressed protein: At3g17210
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / CESG / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


defense response to fungus / defense response to bacterium / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Stress-response A/B barrel domain-containing protein HS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLytle, B.L. / Peterson, F.C. / Volkman, B.F. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biomol.Nmr / Year: 2004
Title: Structure of the hypothetical protein At3g17210 from Arabidopsis thaliana.
Authors: Lytle, B.L. / Peterson, F.C. / Kjer, K.L. / Frederick, R.O. / Zhao, Q. / Thao, S. / Bingman, C. / Johnson, K.A. / Phillips Jr., G.N. / Volkman, B.F.
History
DepositionAug 6, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 19, 2003ID: 1NWJ
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2013Group: Database references / Structure summary
Revision 1.4May 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: expressed protein: At3g17210
B: expressed protein: At3g17210


Theoretical massNumber of molelcules
Total (without water)24,9642
Polymers24,9642
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 / 100LOWEST TARGET FUNCTION
RepresentativeModel #1closest to the average

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Components

#1: Protein expressed protein: At3g17210


Mass: 12482.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (Novagen) / References: UniProt: Q9LUV2

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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
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 1 mM At3g17210 U-15N,13C, 20 MM SODIUM PHOSPHATE BUFFER, 50 MM SODIUM CHLORIDE, 90% H20, 10% D2O
Solvent system: 90% H20, 10% D2O
Sample conditionsIonic strength: 50 mM SODIUM CHLORIDE / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6HERRMANN, T., GUENTERT, P.,refinement
XwinNMR3structure solution
NMRPipe97.027.12.56structure solution
XEASY1.4structure solution
CYANA1.0.6structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF THE TORSION ANGLE DYNAMICS PROGRAM CYANA. ADDITIONAL NOE ASSIGNMENTS WERE DETERMINED MANUALLY AND PEAK INTENSITIES WERE CONVERTED ...Details: INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF THE TORSION ANGLE DYNAMICS PROGRAM CYANA. ADDITIONAL NOE ASSIGNMENTS WERE DETERMINED MANUALLY AND PEAK INTENSITIES WERE CONVERTED INTO UPPER DISTANCE BOUNDS WITH THE CALIBA FUNCTION OF CYANA. THE FINAL STRUCTURES WERE BASED ON THE FOLLOWING RESTRAINTS (FOR EACH MONOMER): 2001 NON-TRIVIAL NOE DISTANCE CONSTRAINTS (1831 INTRAMOLECULAR AND 170 INTERMOLECULAR) AND 141 PHI AND PSI TORSION ANGLE CONSTRAINTS GENERATED FROM CHEMICAL SHIFT DATABASE SEARCHING USING THE PROGRAM TALOS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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