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- PDB-6l7y: Crystal structure of Cet1 from Trypanosoma cruzi in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6l7y
TitleCrystal structure of Cet1 from Trypanosoma cruzi in complex with #466 ligand.
ComponentsmRNA_triPase domain-containing protein
KeywordsHYDROLASE / mRNA capping / RNA triphosphatase
Function / homology
Function and homology information


mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / mRNA processing / nucleus / metal ion binding
Similarity search - Function
RNA 5'-triphosphatase Cet1/Ctl1 / mRNA capping enzyme, beta chain / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / CYTH-like domain superfamily
Similarity search - Domain/homology
3,4,6,7-tetrahydroacridine-1,8(2H,5H)-dione / mRNA 5'-phosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKuwabara, N. / Ho, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H05180 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures of the RNA triphosphatase fromTrypanosoma cruziprovide insights into how it recognizes the 5'-end of the RNA substrate.
Authors: Takagi, Y. / Kuwabara, N. / Dang, T.T. / Furukawa, K. / Ho, C.K.
History
DepositionNov 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA_triPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3976
Polymers23,7971
Non-polymers6005
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.943, 115.943, 56.749
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein mRNA_triPase domain-containing protein


Mass: 23797.006 Da / Num. of mol.: 1 / Mutation: D126N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi strain CL Brener (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053508479.390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E2I1
#2: Chemical ChemComp-JJY / 3,4,6,7-tetrahydroacridine-1,8(2H,5H)-dione


Mass: 215.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.63 Å3/Da / Density % sol: 73.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES-NaOH (pH 7.5), ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.51→49.4 Å / Num. obs: 15320 / % possible obs: 99.7 % / Redundancy: 9.7 % / Biso Wilson estimate: 64.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 16.6
Reflection shellResolution: 2.51→2.61 Å / Rmerge(I) obs: 1.208 / Num. unique obs: 1683 / CC1/2: 0.927 / Rrim(I) all: 1.273

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L7V

6l7v


Resolution: 2.51→49.4 Å / SU ML: 0.3203 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4353
RfactorNum. reflection% reflection
Rfree0.2402 730 4.8 %
Rwork0.2014 --
obs0.2032 15215 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 81.39 Å2
Refinement stepCycle: LAST / Resolution: 2.51→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 36 8 1650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331677
X-RAY DIFFRACTIONf_angle_d0.6272271
X-RAY DIFFRACTIONf_chiral_restr0.0429251
X-RAY DIFFRACTIONf_plane_restr0.0034291
X-RAY DIFFRACTIONf_dihedral_angle_d8.99451386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.70.42331240.34582840X-RAY DIFFRACTION97.69
2.7-2.970.31021570.28882854X-RAY DIFFRACTION98.95
2.97-3.40.29171410.24612881X-RAY DIFFRACTION99.34
3.4-4.290.23521540.18712906X-RAY DIFFRACTION99.84
4.29-49.40.20011540.16523004X-RAY DIFFRACTION99.84
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)
11.435196694450.646145281659-0.800914382836.768589614713.6121536156.428519338020.3213516786781.40920383078-0.399261227346-0.694169284806-0.4950197620070.190885743090.1097729395280.6217299543440.1778175280471.17932512816-0.0831219984016-0.08087506387290.814190025047-0.02784892687650.4515425711198.1338823969104.111387585-11.8223408704
23.85874105704-5.026157819470.9173612530947.79932525613-4.042242066723.709910499460.0379871981123-0.08255862943160.111657247695-0.381717449159-0.09624121560010.0313187364674-0.639182062803-0.3533537972470.129989265790.6926095183550.031254353107-0.0143726932920.652598324415-0.03928323830660.4603734049884.37089240927117.343251449-4.82920052279
37.613059031284.81590677735-1.916657513248.02456135934-1.937685683055.1588798149-0.254263988807-0.17173656653-0.2567395679180.2895551908840.0983846633217-0.5359563696180.1976557215680.1884008615230.1053784859520.6956338419360.0385094541593-0.07838409077870.577127974441-0.0876053785350.60267496529519.1308923873110.1007291489.20800649649
44.75594331108-1.98270117902-2.953972333993.315962303680.2943688201625.302236428110.5115242635670.4175840190560.0586027172447-0.833558269816-0.406183472615-0.964033644049-0.7033996985020.817704723148-0.1234762575570.864128955441-0.1610175534520.142407294080.780922406133-0.04500857627060.81895414349419.0843990983125.8538063144.69944649366
53.071355377162.925437337914.458315511619.145174060711.338031219527.400799916420.06754288665050.264556661442-0.03366129536660.06181619050730.441085292662-0.994785702006-0.2824725770320.639169059234-0.5566193519760.714154055182-0.01427783634730.1001074156530.525175725413-0.1076665446110.64429961571110.2614373862132.85984090812.8748802554
61.26381725607-0.350260363705-0.1923652022162.2054792049-0.3213024879530.9291911976680.171736765150.326602380906-0.241291084753-0.223166071546-0.1513317295450.2804247416950.0950082475810.0889424182004-0.001403909394580.626044098602-0.03843082824630.01777259762980.591502626556-0.0118575826850.5031957674046.52219355779114.2766286821.88226257951
72.70450865091-1.45122140639-2.217043082632.59967458637-0.7510442279494.84626305443-0.282634833395-0.3128437159820.0568285687669-0.3125841725530.368170341294-0.200279206537-0.3807405993180.212652863146-0.03117665699580.654283397418-0.1944382322540.001804092416680.581641567638-0.07254587562710.4965422937199.50254438256129.05233269.9327624932
83.4967075771-2.28560348442-2.722863958385.826276335274.224421161293.43769262938-0.1800282022650.5314245706840.831959167557-0.2263987776990.1006063607-0.4844690620030.8251871169410.122616524968-0.2280146689430.579620881851-0.2019017856760.032395314570.6253174261140.0658208785810.65418278064417.6527494268119.5153135133.42408233534
94.2204561140.225794241261-0.6078818545952.791669240491.187683341164.17366773208-0.1230728098090.009246488823320.37588160507-0.1625809133730.4384845316370.172328296569-1.06342746269-0.341614632765-0.3822987272140.741701967879-0.02001569800450.03978692698140.5718581426250.03612420010580.62462132909912.1536997975118.91777818-0.839351941601
107.48975855614-2.340117998653.98056300784.67779078657-2.710889781552.65197898164-0.1828329119821.1253275214-0.12746815157-0.7370850426380.0967429176196-0.499066418270.8063080313730.7477479400220.03502467971260.7374056837580.01057729757390.1447487146120.659461605594-0.0704371618130.51088653602617.709649116108.216398712-6.57268140005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 189 )
8X-RAY DIFFRACTION8chain 'A' and (resid 190 through 201 )
9X-RAY DIFFRACTION9chain 'A' and (resid 202 through 223 )
10X-RAY DIFFRACTION10chain 'A' and (resid 224 through 241 )

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