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- PDB-7o4f: The DYW domain of A. thaliana OTP86 in its active state -

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Basic information

Entry
Database: PDB / ID: 7o4f
TitleThe DYW domain of A. thaliana OTP86 in its active state
ComponentsPentatricopeptide repeat-containing protein At3g63370, chloroplastic
KeywordsHYDROLASE / cytidine deaminase
Function / homology
Function and homology information


chloroplast RNA processing / RNA modification / chloroplast / mRNA processing / intracellular membrane-bounded organelle / mRNA binding / RNA binding / zinc ion binding
Similarity search - Function
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: 1.65 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
B: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
D: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
G: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,58912
Polymers64,0664
Non-polymers5238
Water6,738374
1
A: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
G: 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
2
B: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
D: 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
Unit cell
Length a, b, c (Å)117.599, 132.883, 30.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-1199-

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.: 4
Source method: isolated from a genetically manipulated source
Details: Protein after TEV cleavage / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PCMP-H83, OTP86, At3g63370, F16M2_220 / Plasmid: pET11-M / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9M1V3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 1.97 Å3/Da / Density % sol: 37 %
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: 7.0 - 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: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→44.03 Å / Num. obs: 57997 / % possible obs: 97.7 % / Redundancy: 12.7 % / Biso Wilson estimate: 18.77 Å2 / CC1/2: 1 / Rrim(I) all: 0.157 / Rsym value: 0.151 / Net I/σ(I): 10.3
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 8940 / CC1/2: 0.764 / Rrim(I) all: 1.802 / Rsym value: 1.724 / % possible all: 94.9

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Processing

Software
NameVersionClassification
XDSMay 15th, 2019data reduction
XSCALEMay 15th, 2019data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292114961

Resolution: 1.65→44.03 Å / SU ML: 0.1978 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2677 2095 3.63 %
Rwork0.2208 55672 -
obs0.2226 57767 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.54 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4428 0 8 375 4811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124530
X-RAY DIFFRACTIONf_angle_d1.21246074
X-RAY DIFFRACTIONf_chiral_restr0.0709647
X-RAY DIFFRACTIONf_plane_restr0.0071778
X-RAY DIFFRACTIONf_dihedral_angle_d25.75971726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.3591280.34943386X-RAY DIFFRACTION90.06
1.69-1.730.35691370.31593638X-RAY DIFFRACTION97.29
1.73-1.780.33081380.33705X-RAY DIFFRACTION98.61
1.78-1.830.30491370.27853628X-RAY DIFFRACTION96.56
1.83-1.890.30061390.27233707X-RAY DIFFRACTION98.89
1.89-1.950.31861370.25663671X-RAY DIFFRACTION96.99
1.95-2.030.24551360.243621X-RAY DIFFRACTION95.65
2.03-2.120.27491400.21473694X-RAY DIFFRACTION98.64
2.12-2.240.2431400.21853722X-RAY DIFFRACTION97.92
2.24-2.380.29271420.21483748X-RAY DIFFRACTION98.28
2.38-2.560.28431410.22273748X-RAY DIFFRACTION98.11
2.56-2.820.2521410.21533718X-RAY DIFFRACTION97.11
2.82-3.220.27921410.22093804X-RAY DIFFRACTION99.22
3.23-4.060.2621440.17913831X-RAY DIFFRACTION97.91
4.06-44.030.22111540.19484051X-RAY DIFFRACTION98.32
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.43256305692-1.03840377535-1.761265729362.9066364592-2.240833558153.42727164746-0.1697997836440.3509551895960.153543174624-0.5153468057060.1426103913150.0522668392687-0.102787065996-0.2221958347760.03648995025130.257218327382-0.07439998500660.06766489804820.127068798504-0.002630992134170.15280113448815.791796296814.7724858796-7.34574172816
23.01505715229-0.0955768719737-0.4093401584164.44466819976-4.014998799894.107421004720.649678961018-0.7379780147480.9519478151210.131168803990.339003576247-0.488903340487-0.649961575603-0.460129621374-0.009622635149310.59229860058-0.194184812466-0.03694226460740.512272409483-0.001098634136730.63748416210221.05512523228.1196173194-11.1350399148
33.855958939212.12513647470.1447913156773.921760057150.6019024657165.84007376170.475972015025-0.08453974236780.615741869607-0.480145724984-0.326140153640.927664245387-2.52214048766-0.962820112911-0.1095536445660.538495501756-0.07987683617540.1141680619620.03692211815010.02753767322340.56182919675711.117717275530.73827277873.6483799348
43.12681316006-3.255886590052.453244758233.63026705499-2.193287714022.83187080771-0.3203180797491.030360708481.46481679-1.341483600480.850298306971-2.17641021517-0.8275686209871.505403594760.4732943021871.32240279043-0.4022399734440.4302224294770.752035616525-0.1923539519650.87620448119633.286859120236.1632625495-0.0398698078148
53.427691236980.2018334002590.3651606835612.43412551756-0.7424876122293.368004403960.0110544462646-0.07638139174230.1590790094510.159099969265-0.03352879473310.090648112458-0.1244359722540.03938743459460.02831151660860.147308770199-0.01859827525060.01610131868410.0804983218746-0.01997338332080.10735733340813.117628102616.34916029495.48038191936
62.195155676881.46442874479-1.698976208132.36646475657-0.5949605145562.19442480288-0.178897348740.105915822919-0.2757140667240.177456924627-0.1214450573460.0862892759578-0.162414466906-0.06953894541320.2198596131130.253201343229-0.0218290344602-0.02514383239250.110700125538-0.01485780679030.17568686124315.4696150964-1.002843112024.27097758562
70.1879596984910.769373160742-0.8153149895583.70577477042-4.003580726274.30654220440.06290676264810.0996716793270.4613344424770.203558537256-1.09270498756-1.172103693271.046636337310.3521816122820.1188718244210.662394904820.06424091732810.2200076472990.6531128980330.1022131298940.88456051234221.1244464067-14.05687185937.86717171827
82.70588867591-0.405460037214-3.257238985475.08241563471-1.19987050115.91725313513-0.589962612552-0.0663606212034-0.619720564183-0.0268686281775-0.6026914492030.7968478679341.9701107809-0.194511188691-0.006151017052410.392335796231-0.02824231928150.04182033677820.1243867990740.0142494545810.4237785208619.19106905604-17.7684132692-4.763949739
98.222640320250.4792044324483.18110574760.763394664851-0.8336695421052.773520049610.4005585268940.467424174543-1.63410382199-0.151328174307-0.3357060939240.289522518196-1.05453011454-0.122649805585-0.4213712431290.700561599040.191077791579-0.1853217552630.346479427422-0.1932230218980.50090270731323.4082183052-19.5936923558-10.0674796907
103.14577377567-4.15124315453.191327618555.73535638298-4.350603565923.31567408609-0.1380854511771.01253294158-0.1428695427191.661992678580.132626809142-2.103817339311.096456617262.43726557070.1140699077360.6752682496860.263019269709-0.1874695325840.938492866623-0.1667998071140.9910406578741.86443978-26.2630816405-1.06320726178
115.01946156097-4.13867509772.547577971834.04224401512-2.461528080781.47843248803-0.434882642443-0.953115102629-1.017720969841.666278979290.4981551451460.4675421873230.6861565778190.29932597969-0.1306789656850.7562318027210.251853829664-0.08569152518560.3180898042850.1245434108640.36531390460226.9586118744-17.8999259338-2.19656771509
122.83412343479-0.016904792304-0.378873963172.03017284874-0.4458953096093.441443147830.01858156715150.0764012141855-0.133186679613-0.0844812430627-0.0511361200585-0.01315466902790.02038535958650.1488075373580.03882582035760.128543709705-0.0229453914728-0.01133546509660.092700416361-0.01903454794420.11548302685813.1762307334-3.24615757671-8.6298153661
134.51309518867-0.889406179932-0.4737544753066.33031922343-0.5708601504077.77265100913-0.165591228008-0.003028473025550.293798595733-0.1823609993720.186393975929-0.324082721285-0.161021161174-0.00718700623767-0.01562766418980.159267903602-0.003649520433120.01695741343510.1244067292690.004613708680540.12316907618743.9583387718-1.43069848797-22.6943149882
142.85891455317-0.181176180423-1.515109861812.506901446231.150167863791.87587897190.75107066018-0.461435295899-0.5197905274120.5016365809320.1214808207220.2878347791450.633333681302-0.98864057825-0.0782561788980.543804334739-0.01610839595260.01490337228730.4144074788550.09084376350690.59064217280837.9608334409-14.9394593228-26.0717272395
154.35475851457-1.00038063783-0.0462781209024.76876573277-2.28637468217.69113857797-0.01689138809030.106240050511-0.721296007317-0.2065596907250.17398272643-0.7413754041751.790721064180.8190434466720.04540265181770.3745958332110.0706992562976-0.04808918675530.122734219930.04205757006320.55041383064750.0100895426-17.8489297472-14.0248062229
169.14627213896-1.278478935821.584770135475.33913903962-0.9441289660056.93017737172-0.110694126398-0.958476465278-0.8550808079050.769007661602-0.0441741831909-0.266511357540.6588762806070.445899450125-0.145530845430.647576468806-0.1544317874160.02848196086960.4370344356490.05518990963720.39603111041142.0622847508-17.358785483-5.15093668782
175.8085647019-4.59028143751-4.437533869183.99369392193.058479427763.97465672365-1.030436321142.36389210379-0.932602167645-1.147149206230.08182485355421.470988812690.293102567341-2.248516838430.4917375153461.18819734633-0.214081303761-0.2206590297170.898461346977-0.05950048320930.7922759141220.6663652199-25.7308531891-14.5573492993
182.594684434562.421079097521.430771597345.987975137842.313406945750.930890376422-0.1255416066180.179706519259-0.499094230627-1.180863264090.4289972709720.2887118617661.231398466570.396704132890.1843017163840.823767635496-0.1251898490830.01953189586730.2564108619990.02453376580420.41905848826531.1273519946-19.6590113862-15.8522592917
193.405534490880.499473463212-1.233280870661.27059187086-0.1401176299911.8818288076-0.09166878942160.0255065154164-0.197912698602-0.08304791832250.0377320362901-0.07332190608780.008452127878770.02863384895110.09615158373510.136864073863-0.0175185959417-0.01216770084990.1162788520470.002887959662720.15996655631646.637199361-4.55702467462-15.4557940654
202.94162100941-0.0760452519969-0.2007862411722.496738840410.01909021096073.07166085013-0.0119494566675-0.258711723823-0.1438288688390.107860967056-0.119836965214-0.1021667349170.03436653530350.04477947458830.07139201274140.12272008773-0.0122689064954-0.02724571077340.1609358731520.02272014913070.11592992059345.0556760437-2.47899073511-5.7519622353
212.29430398764-2.33249276647-2.759561710485.090848540552.98186418823.50910641163-0.34654723883-0.303939225697-0.04393199967780.3208095636960.461909276542-0.2566253707160.283385633413-0.0166147653063-0.01781740935550.208776201357-0.0415666706651-0.04994060659230.2087438732310.02307274780020.18787278422843.383559244314.174557627619.6365222849
225.700748696335.251533796751.297249851395.115646121331.792002021212.243528382720.472785524011-1.37459972731.957886312321.1436012860.369529126177-0.570692966049-0.9762775087210.282377391114-0.8510680527330.778655389140.092298174935-0.03556066935950.68695905512-0.1781524439550.79280322674837.471531863927.243780561423.3718695564
234.997605020111.707695273720.5730307739093.47935725219-0.4804559280722.196747062740.00624105841567-0.2248400256461.46509123680.831738339405-0.354426235138-1.15569424392-2.269767109360.3263397909930.05149890702110.713458166544-0.08811553730270.09164793600820.170067526170.1230695157230.82078132335849.71125628430.865394489511.1715766273
244.109531729621.35325997599-0.01776878907880.7868486152461.422965253658.15785878721-0.3722743118410.06278632680911.07901343408-0.454844886835-0.4412450011040.195780824107-1.58418553433-0.8008151824010.2773522323060.674527573440.1298357119440.009751284281370.402751722130.05959431406870.80638051917142.425230197431.08782686461.80135464712
255.242056020313.716234550362.853023625656.01905237588-0.2980753471912.014900142320.358487802076-0.977171644531.596973146330.6619622701270.7212051464960.993350942698-0.598732070481-2.550286076240.2257943332880.8926665078420.1020911880870.1087877818430.4628506488960.01354904121540.6180476585121.218698422237.57644283312.4724325509
267.76450200495-0.0245157211042-1.717598671626.674235612522.887797805882.47419930568-1.11572560385-0.6832073252050.904796434061.839769007120.157589400591-0.320593517204-0.0104517732966-0.0848347748875-0.07062728258370.9332559288750.460939599466-0.0921751891333-0.101952736920.104244886950.4295699156530.514974062431.96827543813.4485455238
273.94470150279-0.6223382663310.8670771120752.054993087820.04473290380674.005181200060.004646999428310.1093005989060.232682822515-0.0556000316578-0.0320941236321-0.109099652862-0.1724776721220.05049449811330.03014680200920.174789567647-0.005238433528710.0182091511060.11282371440.02304335221960.13971934716245.561944327316.26491895566.84967692271
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 825 through 840 )AA825 - 8401 - 16
22chain 'A' and (resid 841 through 849 )AA841 - 84917 - 25
33chain 'A' and (resid 850 through 874 )AA850 - 87426 - 50
44chain 'A' and (resid 875 through 892 )AA875 - 89251 - 68
55chain 'A' and (resid 893 through 960 )AA893 - 96069 - 136
66chain 'B' and (resid 825 through 839 )BD825 - 8391 - 15
77chain 'B' and (resid 840 through 849 )BD840 - 84916 - 25
88chain 'B' and (resid 850 through 867 )BD850 - 86726 - 43
99chain 'B' and (resid 868 through 877 )BD868 - 87744 - 53
1010chain 'B' and (resid 878 through 885 )BD878 - 88554 - 61
1111chain 'B' and (resid 886 through 892 )BD886 - 89262 - 68
1212chain 'B' and (resid 893 through 960 )BD893 - 96069 - 138
1313chain 'D' and (resid 826 through 840 )DG826 - 8401 - 15
1414chain 'D' and (resid 841 through 849 )DG841 - 84916 - 24
1515chain 'D' and (resid 850 through 866 )DG850 - 86625 - 41
1616chain 'D' and (resid 867 through 874 )DG867 - 87442 - 49
1717chain 'D' and (resid 875 through 884 )DG875 - 88450 - 59
1818chain 'D' and (resid 885 through 892 )DG885 - 89260 - 67
1919chain 'D' and (resid 893 through 920 )DG893 - 92068 - 99
2020chain 'D' and (resid 921 through 960 )DG921 - 960100 - 139
2121chain 'G' and (resid 825 through 839 )GJ825 - 8391 - 15
2222chain 'G' and (resid 840 through 849 )GJ840 - 84916 - 25
2323chain 'G' and (resid 850 through 866 )GJ850 - 86626 - 42
2424chain 'G' and (resid 867 through 873 )GJ867 - 87343 - 49
2525chain 'G' and (resid 874 through 884 )GJ874 - 88450 - 60
2626chain 'G' and (resid 885 through 892 )GJ885 - 89261 - 68
2727chain 'G' and (resid 893 through 960 )GJ893 - 96069 - 136

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