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- PDB-7o4e: The DYW domain of A. thaliana OTP86 in its inactive state -

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Basic information

Entry
Database: PDB / ID: 7o4e
TitleThe DYW domain of A. thaliana OTP86 in its inactive state
ComponentsPentatricopeptide repeat-containing protein At3g63370, chloroplastic
KeywordsHYDROLASE / cytidine deaminase
Function / homology
Function and homology information


chloroplast RNA processing / RNA modification / chloroplast / mRNA processing / mRNA binding / zinc ion binding
Similarity search - Function
E motif / E+ motif / : / E+ motif / E motif / DYW domain / DYW family of nucleic acid deaminases / PPR repeat / PPR repeat family / Pentatricopeptide (PPR) repeat profile. ...E motif / E+ motif / : / E+ motif / E motif / DYW domain / DYW family of nucleic acid deaminases / PPR repeat / PPR repeat family / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWeber, G. / Palm, G.J. / Takenaka, M. / Barthel, T. / Feiler, C. / Weiss, M.S.
CitationJournal: Nat Catal / Year: 2021
Title: DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis.
Authors: Takenaka, M. / Takenaka, S. / Barthel, T. / Frink, B. / Haag, S. / Verbitskiy, D. / Oldenkott, B. / Schallenberg-Rudinger, M. / Feiler, C.G. / Weiss, M.S. / Palm, G.J. / Weber, G.
History
DepositionApr 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 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 At3g63370, chloroplastic
B: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2956
Polymers32,0332
Non-polymers2624
Water59433
1
A: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
hetero molecules

A: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2956
Polymers32,0332
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
2
B: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
hetero molecules

B: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2956
Polymers32,0332
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)124.570, 30.580, 77.530
Angle α, β, γ (deg.)90.000, 125.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-885-

LYS

21B-1115-

HOH

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Components

#1: Protein Pentatricopeptide repeat-containing protein At3g63370, chloroplastic / Protein ORGANELLE TRANSCRIPT PROCESSING 86


Mass: 16016.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PCMP-H83, OTP86, At3g63370, F16M2_220 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9M1V3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 nl protein plus 100 nl reservoir (0.1 M glycine, pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4) plus 30 nl additive (0.1 M 50% v/v Jeffamine M-600 pH 7.0). Cryo: reservoir solution ...Details: 100 nl protein plus 100 nl reservoir (0.1 M glycine, pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4) plus 30 nl additive (0.1 M 50% v/v Jeffamine M-600 pH 7.0). Cryo: reservoir solution supplemented with 15% (v/v) ethylene glycol.
PH range: 7.9 - 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.5→80 Å / Num. obs: 16019 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.3 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.235 / Rsym value: 0.216 / Net I/σ(I): 7.46
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.06 / Num. unique obs: 1761 / CC1/2: 0.428 / Rrim(I) all: 1.899 / Rsym value: 1.734 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSJanuary 26th, 2018data reduction
XDSJanuary 26th, 2018data scaling
PHASERphasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_129211461

Resolution: 2.5→38.722 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 425 5.01 %
Rwork0.2215 8057 -
obs0.2241 8482 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.8 Å2 / Biso mean: 48.7795 Å2 / Biso min: 26.76 Å2
Refinement stepCycle: final / Resolution: 2.5→38.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 4 33 2136
Biso mean--58.11 42.86 -
Num. residues----257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.86170.33821400.25792641100
2.8617-3.6050.26111390.24682663100
3.605-38.720.25931460.2001275399

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