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- PDB-6ywo: CutA in complex with A3 RNA -

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Basic information

Entry
Database: PDB / ID: 6ywo
TitleCutA in complex with A3 RNA
Components
  • CutA
  • RNA (5'-R(*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN / terminal nucleotide transferase / polymerase / RNA-binding protein
Function / homologyTUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / poly(A) RNA polymerase activity / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily / RNA / Uncharacterized protein
Function and homology information
Biological speciesThermothielavioides terrestris NRRL 8126 (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMalik, D. / Kobylecki, K. / Krawczyk, P. / Poznanski, J. / Jakielaszek, A. / Napiorkowska, A. / Dziembowski, A. / Tomecki, R. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish SciencePOIR.04.04.00-00-20E7/16-00 Poland
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine.
Authors: Malik, D. / Kobylecki, K. / Krawczyk, P. / Poznanski, J. / Jakielaszek, A. / Napiorkowska, A. / Dziembowski, A. / Tomecki, R. / Nowotny, M.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CutA
B: CutA
C: CutA
D: CutA
E: RNA (5'-R(*AP*AP*A)-3')
I: RNA (5'-R(*AP*AP*A)-3')
F: RNA (5'-R(*AP*AP*A)-3')
K: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,21822
Polymers173,8558
Non-polymers36314
Water17,997999
1
A: CutA
F: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5485
Polymers43,4642
Non-polymers843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-31 kcal/mol
Surface area16270 Å2
MethodPISA
2
B: CutA
E: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5967
Polymers43,4642
Non-polymers1335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-40 kcal/mol
Surface area16160 Å2
MethodPISA
3
C: CutA
I: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5124
Polymers43,4642
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-20 kcal/mol
Surface area16090 Å2
MethodPISA
4
D: CutA
K: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5616
Polymers43,4642
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-29 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.920, 56.950, 149.890
Angle α, β, γ (deg.)79.859, 87.116, 75.832
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
CutA


Mass: 42521.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothielavioides terrestris NRRL 8126 (fungus)
Gene: THITE_2112714 / Plasmid: pet28SUMO
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): RIL / References: UniProt: G2R014
#2: RNA chain
RNA (5'-R(*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate monohydrate and 25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→33.26 Å / Num. obs: 136433 / % possible obs: 96.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.71 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.49
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 21579 / CC1/2: 0.59 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: XXXX

Resolution: 1.9→33.26 Å / SU ML: 0.2405 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.8665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 6817 5 %
Rwork0.1758 129557 -
obs0.1777 136374 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11133 252 14 999 12398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008811799
X-RAY DIFFRACTIONf_angle_d0.945316091
X-RAY DIFFRACTIONf_chiral_restr0.05511829
X-RAY DIFFRACTIONf_plane_restr0.00552040
X-RAY DIFFRACTIONf_dihedral_angle_d22.71244437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39292040.35653895X-RAY DIFFRACTION88.53
1.92-1.940.33032300.29744364X-RAY DIFFRACTION95.61
1.94-1.970.352290.2834344X-RAY DIFFRACTION95.43
1.97-1.990.27622220.25464226X-RAY DIFFRACTION95.8
1.99-2.020.28192260.23944288X-RAY DIFFRACTION95.8
2.02-2.040.26382300.22334370X-RAY DIFFRACTION95.67
2.04-2.070.26542210.22274200X-RAY DIFFRACTION95.36
2.07-2.110.27262300.21934366X-RAY DIFFRACTION95.45
2.11-2.140.27182210.21574202X-RAY DIFFRACTION95.04
2.14-2.170.25172280.20814326X-RAY DIFFRACTION95.77
2.17-2.210.25322280.20054340X-RAY DIFFRACTION96.58
2.21-2.250.22762280.18094336X-RAY DIFFRACTION96.17
2.25-2.290.24042300.18074361X-RAY DIFFRACTION96.82
2.29-2.340.22982250.17594283X-RAY DIFFRACTION96.12
2.34-2.390.22982300.17384363X-RAY DIFFRACTION96.74
2.39-2.450.23182280.18134337X-RAY DIFFRACTION96.8
2.45-2.510.26262300.18454374X-RAY DIFFRACTION97.13
2.51-2.580.2332310.18074384X-RAY DIFFRACTION96.93
2.58-2.650.24342270.17844305X-RAY DIFFRACTION97
2.65-2.740.23012300.17054377X-RAY DIFFRACTION96.68
2.74-2.840.21142310.16784388X-RAY DIFFRACTION96.71
2.84-2.950.19392270.16884312X-RAY DIFFRACTION97.36
2.95-3.080.20652310.16934379X-RAY DIFFRACTION97.4
3.08-3.250.19252300.17024381X-RAY DIFFRACTION97.71
3.25-3.450.21122330.16064417X-RAY DIFFRACTION97.71
3.45-3.710.18022280.15694335X-RAY DIFFRACTION96.57
3.71-4.090.18272270.14644322X-RAY DIFFRACTION94.99
4.09-4.680.16072300.13894369X-RAY DIFFRACTION98.02
4.68-5.890.19642280.16794337X-RAY DIFFRACTION96.96
5.89-33.260.19832240.19254276X-RAY DIFFRACTION94.86
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)
12.80243656717-0.8429670471.373787595045.28131351771-2.442344861817.866479316590.00745383187627-0.5769843025340.16717987660.8418024449180.1175957860273.3345983272E-5-0.382759776019-0.227069489474-0.1003926881610.339754821821-0.02091752560440.06207730325050.315827493594-0.1512911202690.31554362383-3.590058508312.642255635634.3575682052
23.08252828118-2.074147977061.267852732163.30024249722-1.689450353571.10521501930.1040758222410.1410218946170.0453674338208-0.195050925579-0.0936022387417-0.08253133068430.01570628839890.115844674411-0.007627569224730.266129297330.01631892670010.02422886094260.351070374165-0.02290047319360.2313507239620.0638179343-3.3125686401820.6672493789
31.463325026030.2115330395280.09601545096021.60450306749-0.2871347224031.467760323140.0211798345437-0.01044580638980.02801020214750.00450062549297-0.0223083192126-0.03259599771690.0690896847419-0.0006376120365650.002602987584660.1950500097720.02204646169110.004097090210870.235442164585-0.008188839847690.221288294416-2.092662219141.959180280521.0121807419
43.75439513761-0.704577397474-2.153965754133.9539757377-0.2494164131616.855236863760.1950062426060.5119834478650.371171417037-0.697053613415-0.04254727182620.185020296577-0.74452592633-0.334385625464-0.1264707850050.3459991069160.0495400733676-0.1298327166650.321718158630.1095212670020.363278782721-5.6276936677514.6487232638-29.8371761784
51.97548521264-1.21951574587-1.104049761163.70773174471.372752533261.29669115927-0.0713642249424-0.119756437485-0.08554392807540.1014088566610.0990839888070.06973895331360.116261820375-0.0229693512533-0.03707879018840.377105983613-0.0216292423875-0.01212182758470.2523266955780.02818060211610.237399608864.06796840019-15.3719143948-17.2159409105
61.63663221948-0.112347625275-0.2663238895171.076447510230.1329208097951.222186263370.001240982843420.016893875685-0.00529322806676-0.03125721620610.02108863890080.0540961844410.01088717395590.0244655098671-0.02670898755240.221625703580.00503355979872-0.01461479307120.1363447424310.005448733477210.1853430571794.585514831557.29158519857-17.5991992879
73.192729220021.06358508242-0.9826888834043.63197444995-0.6443724144623.723063645570.279086710023-0.6066864330550.4131687679630.135652749663-0.342923925078-0.248862191859-0.7620419491520.7184335032480.07613168897420.493701020998-0.1947972629780.03687596292120.506387901218-0.05317196692020.30103692240822.7684779932-3.9313457453460.7222471177
84.51637366368-0.1599734230175.353938517552.875878924090.4525234857386.43282132566-0.327060459233-1.32601293153-0.3208947346650.804388494081-0.517767528747-0.230910581965-0.1564480667580.3439672811710.581753722730.600446188731-0.1581690628810.003740622997831.068578821030.2477727415390.41449802353110.4004338569-21.51718858873.8515063247
96.953203991380.8835711214234.082476280783.407198751710.9360834972192.450024226960.556586594074-0.55142556174-0.6205905648080.783393269219-0.353608378127-0.4291758494320.769166539128-0.522936155143-0.2580188506940.362013685143-0.115280183946-0.05859441421820.2657942205550.01915289899250.33164887952-12.0313108415-27.165600729350.280959637
106.37152731744-0.1939442674042.377766868782.03220917169-1.632080783722.11505546051-0.0125598113471-0.067721501077-0.277514092415-0.022180831757-0.000166114569334-0.0633300657077-0.0129349548327-0.02816372105570.004135173366140.1797510643860.004505775643970.02328720388310.187552001073-0.05425143277910.227872585243-6.45041835266-23.785905993742.8890078976
115.77056132929-0.6988455896111.659907877693.195999022640.0835019254744.247327533650.0241320632466-0.0542542333954-0.1218049421540.143190275699-0.105358260985-0.00757228918867-0.130844433149-0.07929825984310.03287105462360.225397494376-0.0100116711734-0.03249662059170.189612895252-0.017409900980.259736729264-8.12482926302-16.529467276745.4958097593
128.871601754220.1769475583222.623070900312.75050626842-0.1684568290845.87635380524-0.0273970575874-0.0174407793514-1.02556501304-0.239528637301-0.278400736477-0.2805335035870.4587576907750.202934048430.2714492321680.272734588936-0.01875807334110.02948900569150.2194414189360.02350736513690.5199023166129.65366523277-29.805336395549.9683274093
133.442361409060.442414849389-0.5510124955691.396299727150.4240055242872.511511834510.0674849246976-0.508072981048-0.7378678008540.258530259-0.237226802012-0.1270429400730.1955670708080.119710602670.1296552210630.250951400969-0.0181120815341-0.02590289306160.3461071995740.1429557174240.33687407817418.3401129655-23.076600344456.5236630488
143.773007123080.367430047121-2.571070829242.25267842334-0.5233478200353.488182402710.009545647357330.292113935865-0.218101729022-0.126619743322-0.09802263966810.1276847906450.00289241324388-0.1790115251370.0855846471250.2201650297280.0128654825407-0.030933872220.312564534649-0.001977459705390.22082314750920.6593461477-14.54832276342.5025977843
152.89142870820.529921508077-0.6670953132442.61773413583-0.2357920020147.140720732780.390807944602-0.9658286124440.3716006822870.581133937449-0.3273784909590.167863046-0.849426570587-0.00610146213099-0.07590491119650.494800692611-0.1326367406540.04921254404630.531992781448-0.1085648888170.29511969809715.8179661185-5.7808582065964.3228527993
162.558168264461.62459391781-0.294938901371.5959117252-0.4569321950553.67048437884-0.5286660917790.7772000767380.199794869164-0.5845589236840.3754887567440.01336351989410.235224527899-0.300724627930.148294289910.554587499809-0.07992265769020.01678724291730.5458339753490.08672734704890.33165742782113.8027304032-14.8842064009-63.783787995
174.206031481310.4672705774830.7606856320254.115570207031.560739953174.0060799282-0.04457501895310.25245129202-0.191601624632-0.02034512904570.0244740633903-0.03249126945450.03325513305410.06380218630740.01155565593410.219332921184-0.0245933792997-0.02345071430460.1771994490070.02907770274530.24595523452429.35931965497.2109499139-41.9665195972
182.730541210290.574195080652-0.303266568063.11088890697-0.564364645172.50448584179-0.1698366138490.3101344060.0919887306956-0.2114048431570.0422526713119-0.355984517211-0.01935268177530.01145760741450.1185678889730.285101551702-0.03091710419120.03114929372340.196848527725-0.008185073328240.23123191937420.8414863924-16.9115890186-51.7164927997
193.37184236269-1.08433486185-2.277767968441.193284130652.319203099974.631451087320.9220590393080.544638590434-0.320049828321-1.290787537970.002047179512590.3031146742610.1067471211830.356586180268-0.8969386089931.848346780080.512222199166-0.03204791354671.307058308520.111690984730.6963113186129.09743948414-7.05880909616-25.6715053802
209.30709547008-5.27988923227-3.66156802313.634139544160.2168621827586.82511264872-0.4662423822320.3952312315680.567793830361-1.37529313591-0.2510921717292.5167759382-1.44757089027-0.9001249367090.60271982061.16779526292-0.108009359537-0.6118776763330.8668068105310.2296973199141.797451191954.44814137333-15.543457689144.6513682549
217.342704652251.6781573628-1.950739478672.27393885499-0.2146787774880.5471619610170.168608821538-1.58782813847-0.07654735655431.231751198081.02929360944-0.2460850560861.32550090431-1.25538587167-1.131624769981.00231123430.230933620972-0.01272784512591.254182068530.1238923018730.58198011975810.6669347337-5.9137694038728.9403843649
226.235406351120.4687352999420.1614563378391.35838435764-1.146992448441.462753387420.02810346300430.02625185656970.382234002232-0.0556256421163-0.3973181163780.8268215827430.291409164916-0.4977563281690.3418439062360.695144980771-0.1456829656560.01959289723621.1606789417-0.2199504725450.95571893965519.9365532282-3.33783086379-41.2472164315
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 245 through 273 )AA245 - 2731 - 31
22chain 'A' and (resid 274 through 397 )AA274 - 39732 - 163
33chain 'A' and (resid 398 through 598 )AA398 - 598164 - 374
44chain 'B' and (resid 246 through 273 )BB246 - 2731 - 30
55chain 'B' and (resid 274 through 397 )BB274 - 39731 - 156
66chain 'B' and (resid 398 through 598 )BB398 - 598157 - 361
77chain 'C' and (resid 247 through 273 )CC247 - 2731 - 27
88chain 'C' and (resid 274 through 294 )CC274 - 29428 - 50
99chain 'C' and (resid 295 through 315 )CC295 - 31551 - 71
1010chain 'C' and (resid 316 through 363 )CC316 - 36372 - 119
1111chain 'C' and (resid 364 through 397 )CC364 - 397120 - 153
1212chain 'C' and (resid 398 through 413 )CC398 - 413154 - 169
1313chain 'C' and (resid 414 through 534 )CC414 - 534170 - 288
1414chain 'C' and (resid 535 through 564 )CC535 - 564289 - 322
1515chain 'C' and (resid 565 through 597 )CC565 - 597323 - 355
1616chain 'D' and (resid 248 through 294 )DD248 - 2941 - 49
1717chain 'D' and (resid 295 through 397 )DD295 - 39750 - 154
1818chain 'D' and (resid 398 through 597 )DD398 - 597155 - 362
1919chain 'E' and (resid -2 through 0 )EE-2 - 0
2020chain 'I' and (resid -2 through 0 )IF-2 - 0
2121chain 'F' and (resid -2 through 0 )FG-2 - 0
2222chain 'K' and (resid -2 through 0 )KH-2 - 0

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