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- PDB-7w86: Crystal structure of the DYW domain of DYW1 -

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Basic information

Entry
Database: PDB / ID: 7w86
TitleCrystal structure of the DYW domain of DYW1
ComponentsPentatricopeptide repeat-containing protein DWY1, chloroplastic
KeywordsRNA / RNA editing / post-transcriptional modification
Function / homology
Function and homology information


chloroplast mRNA modification / chloroplast RNA modification / plastid / chloroplast / mRNA processing / zinc ion binding
Similarity search - Function
DYW domain / DYW family of nucleic acid deaminases
Similarity search - Domain/homology
ACETATE ION / Pentatricopeptide repeat-containing protein DWY1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSawada, Y. / Shimizu, H. / Toma-Fukai, S. / Shimizu, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Japan Agency for Medical Research and Development (AMED) Japan
Japan Science and Technology Japan
CitationJournal: Plant Cell / Year: 2023
Title: Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation.
Authors: Toma-Fukai, S. / Sawada, Y. / Maeda, A. / Shimizu, H. / Shikanai, T. / Takenaka, M. / Shimizu, T.
History
DepositionDec 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentatricopeptide repeat-containing protein DWY1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,97122
Polymers13,5131
Non-polymers1,45821
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area7030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.945, 45.165, 37.023
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pentatricopeptide repeat-containing protein DWY1, chloroplastic / DYW-domain protein 1


Mass: 13512.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DYW1, PCMP-H50, At1g47580, F16N3.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7R1

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Non-polymers , 6 types, 57 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes pH 7.5, 0.1 M Sodium Acetate, 0.2 M Lithium sulfate, 25%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.28242 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28242 Å / Relative weight: 1
ReflectionResolution: 1.8→45.17 Å / Num. obs: 10107 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 616 / CC1/2: 0.625

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→36.66 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.435 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23365 507 5 %RANDOM
Rwork0.17729 ---
obs0.18029 9586 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.03 Å2
2---0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 84 36 1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131027
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151024
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.6651349
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5952356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4920.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6515188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.833159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1242.6472
X-RAY DIFFRACTIONr_mcbond_other2.1042.58468
X-RAY DIFFRACTIONr_mcangle_it3.1093.863585
X-RAY DIFFRACTIONr_mcangle_other3.1083.863586
X-RAY DIFFRACTIONr_scbond_it3.6233.368555
X-RAY DIFFRACTIONr_scbond_other3.623.371556
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4514.749764
X-RAY DIFFRACTIONr_long_range_B_refined7.08632.2511128
X-RAY DIFFRACTIONr_long_range_B_other7.08432.2891129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 27 -
Rwork0.288 719 -
obs--100 %

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