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- PDB-6ywn: CutA in complex with CMPCPP -

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Basic information

Entry
Database: PDB / ID: 6ywn
TitleCutA in complex with CMPCPP
ComponentsCutA
KeywordsRNA BINDING PROTEIN / terminal nucleotide transferase / polymerase / RNA-binding protein
Function / homology
Function and homology information


RNA 3'-end processing / poly(A) RNA polymerase activity / metal ion binding
Similarity search - Function
TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-2TM / Uncharacterized protein
Similarity search - Component
Biological speciesThermothielavioides terrestris NRRL 8126 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0423
Polymers42,5211
Non-polymers5212
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.220, 93.470, 86.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein CutA


Mass: 42521.148 Da / Num. of mol.: 1
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2TM / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine / CMPcPP


Mass: 481.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium formate and 20% 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: 1.45→32.08 Å / Num. obs: 63468 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 18.95 Å2 / CC1/2: 0.99 / Net I/σ(I): 13
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 12.2 % / Num. unique obs: 10054 / CC1/2: 0.65 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
PHENIX1.18_3861refinement
XDS1.17.1_3660data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: XXXX

Resolution: 1.45→32.08 Å / SU ML: 0.1282 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 3172 5 %
Rwork0.1561 60295 -
obs0.1574 63467 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.63 Å2
Refinement stepCycle: LAST / Resolution: 1.45→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 30 375 3203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182986
X-RAY DIFFRACTIONf_angle_d1.20614072
X-RAY DIFFRACTIONf_chiral_restr0.0871459
X-RAY DIFFRACTIONf_plane_restr0.0081521
X-RAY DIFFRACTIONf_dihedral_angle_d25.4436419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.27861290.26682477X-RAY DIFFRACTION95.07
1.47-1.490.28681380.24572615X-RAY DIFFRACTION99.89
1.49-1.520.28681360.24432578X-RAY DIFFRACTION99.49
1.52-1.550.27191360.21432599X-RAY DIFFRACTION99.93
1.55-1.570.22481370.20692604X-RAY DIFFRACTION100
1.57-1.60.23291370.19112601X-RAY DIFFRACTION99.96
1.6-1.640.19761380.18142625X-RAY DIFFRACTION100
1.64-1.670.21321360.17352582X-RAY DIFFRACTION100
1.67-1.710.21511380.16822608X-RAY DIFFRACTION99.89
1.71-1.750.20341370.16282602X-RAY DIFFRACTION100
1.75-1.80.19171390.15712638X-RAY DIFFRACTION99.89
1.8-1.850.16911360.15072600X-RAY DIFFRACTION99.85
1.85-1.910.18531370.14782595X-RAY DIFFRACTION99.67
1.91-1.980.17961380.14562618X-RAY DIFFRACTION100
1.98-2.060.17331390.13832649X-RAY DIFFRACTION100
2.06-2.160.18251380.13542620X-RAY DIFFRACTION100
2.16-2.270.1651380.1362620X-RAY DIFFRACTION99.89
2.27-2.410.16941390.13422638X-RAY DIFFRACTION100
2.41-2.60.14461390.13992654X-RAY DIFFRACTION99.71
2.6-2.860.17681390.14752626X-RAY DIFFRACTION99.42
2.86-3.270.16011400.15032674X-RAY DIFFRACTION99.93
3.27-4.120.14161420.14072685X-RAY DIFFRACTION99.86
4.12-32.080.21511460.17442787X-RAY DIFFRACTION99.52
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.052491961010.09869261310231.519873013621.50508009634-0.5645866346835.64805912298-0.007551785217390.739588186116-0.00211102452683-0.1128599171790.0746470620040.13436459726-0.150831921653-0.153816192449-0.06337203613230.282315077522-0.0167919853915-0.0185014563457-0.03447495919570.005629958679150.216322758223-22.5664972315-0.278587072151-29.579310049
28.525863001617.49925813317-6.694749329577.24077590225-6.115786978735.325721740420.154671550059-0.07858139350270.1729809838090.176310634125-0.0698693365435-0.151216688884-0.17748480340.258935375729-0.0704220095610.2104332022160.00421726314694-0.02510440243710.2001173810260.006537515144320.199542369694-10.3485499475-4.55660526938-7.42617529358
34.548527606032.66829930597-0.6096428733562.91508031987-0.1035055273711.05341076830.00393923538676-0.183511491392-0.3521988418640.131944806536-0.101189782059-0.1422692894330.0884469719066-0.08914651174670.08508853974410.1426987907260.01660055039530.0004075447967780.1461572675480.02889419605010.133387187779-35.5140945375-25.8507105813-0.927508842938
44.978346798251.17688617165-1.213761234573.985018495250.7040160430184.98578116895-0.01974396395620.2257693721810.01157828066510.116624027005-0.1321374106980.08324584850820.0931101911436-0.302366631450.1482093654860.1510270000570.05587666007290.01042905321750.260516073660.002613336797510.227788703522-47.7890098552-21.7582136149-4.03295037121
55.158437290751.77227782521-0.07287544475257.496814042143.692359615764.0748637108-0.0226452987301-0.1330074617470.1250446945050.0859121769559-0.0815854175630.03950587977090.103388724705-0.07184055432270.1235556414610.1638560101070.0298571190314-0.0005684135250640.1933339246430.02873970202940.165597163658-39.1735765694-19.0750203649-2.44335362404
60.7864660051690.184683685389-0.01656097846292.47166550872-0.1331797632140.85903931076-0.031483799435-0.001185337807550.01780222070240.05994131878070.0176270484840.1245380084-0.0194864503204-0.07452392462110.01858327812040.1579934814550.006723928499960.002939170715550.1653183496635.5260640899E-50.149766480432-22.7724200659-15.5015293568-15.0914216051
71.725807810071.34749679148-0.1351844051834.17682495478-0.6828859181110.919708033611-0.09961082433290.0708972004356-0.136962108867-0.1446257757690.0415933627998-0.2374331807160.1271147374880.06543639613030.06093393347210.1782256281880.02131594426680.01838155052660.161070419687-0.02636776397420.176890921164-16.9782375001-31.8729576429-18.7708551239
80.8215412993760.3703079564740.1622180438861.73018424514-0.3655455789890.863072297687-0.03844713449680.142489039993-0.027575673609-0.06059064104740.0180595524203-0.1473526319710.06775296874420.07369762879390.02823117654620.1510556294940.004203400419730.02069786359110.184364029406-0.005393299195760.171461422426-14.9973908507-16.2498922973-24.299325921
91.062086398460.1994462601530.6118876425520.86250738386-0.2197787184441.824422407360.02150762730450.105340658923-0.0492596787095-0.026484213708-0.04425022880890.1459885881430.107949714709-0.07584411408820.0256811130240.169428233864-0.0206314788709-0.01665942937070.2165238568720.007895107931060.207941045024-31.5140964764-18.9367991171-29.7291872288
102.749086598680.3240084004630.833933773551.896736611020.05111740242712.28431563092-0.1627858174410.002860109842110.215325606564-0.01322579757070.04214073641580.133845286486-0.273377055968-0.08643960117170.1120707382430.222557004070.0147879084038-0.01554694491790.131733494040.009458944819730.225879917278-23.10917184010.963616948714-20.9615523915
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 248 through 273 )248 - 2731 - 26
22chain 'A' and (resid 274 through 294 )274 - 29427 - 51
33chain 'A' and (resid 295 through 353 )295 - 35352 - 117
44chain 'A' and (resid 354 through 378 )354 - 378118 - 146
55chain 'A' and (resid 379 through 397 )379 - 397147 - 167
66chain 'A' and (resid 398 through 457 )398 - 457168 - 229
77chain 'A' and (resid 458 through 487 )458 - 487230 - 263
88chain 'A' and (resid 488 through 534 )488 - 534264 - 314
99chain 'A' and (resid 535 through 564 )535 - 564315 - 350
1010chain 'A' and (resid 565 through 596 )565 - 596351 - 384

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