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- PDB-6l7x: Crystal structure of Cet1 from Trypanosoma cruzi in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6l7x
TitleCrystal structure of Cet1 from Trypanosoma cruzi in complex with #951 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 / metal ion binding / nucleus
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
1,3-dimethyl-7-propyl-purine-2,6-dione / mRNA 5'-phosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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)24,4046
Polymers23,7971
Non-polymers6065
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-15 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.673, 114.673, 56.666
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-E7R / 1,3-dimethyl-7-propyl-purine-2,6-dione


Mass: 222.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O2 / 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.: 27 / 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: 4.62 Å3/Da / Density % sol: 73.37 %
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: 2.39→49.65 Å / Num. obs: 17359 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 56.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.106 / Net I/σ(I): 14.8
Reflection shellResolution: 2.39→2.48 Å / Rmerge(I) obs: 1.86 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1792 / CC1/2: 0.776 / Rrim(I) all: 1.953

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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: 2.39→49.65 Å / SU ML: 0.3272 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3007
RfactorNum. reflection% reflection
Rfree0.2382 807 4.68 %
Rwork0.2039 --
obs0.2056 17245 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.33 Å2
Refinement stepCycle: LAST / Resolution: 2.39→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 36 27 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291673
X-RAY DIFFRACTIONf_angle_d0.69822264
X-RAY DIFFRACTIONf_chiral_restr0.0404250
X-RAY DIFFRACTIONf_plane_restr0.0023289
X-RAY DIFFRACTIONf_dihedral_angle_d8.6191996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.540.31891260.31252705X-RAY DIFFRACTION99.75
2.54-2.740.36661360.2932707X-RAY DIFFRACTION99.48
2.74-3.010.33371070.27372725X-RAY DIFFRACTION99.72
3.01-3.450.30111410.24062727X-RAY DIFFRACTION99.93
3.45-4.340.21351490.18322740X-RAY DIFFRACTION100
4.34-49.650.19141480.162834X-RAY DIFFRACTION99.87
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)
16.36131049436-0.466980502855-2.801209692673.71132980105-0.6068658898494.997612266980.2838686655340.632419810972-0.296912123943-0.0759700918143-0.384882790496-0.1549741231940.06869858257230.27356266863-0.07201793486490.7262144329810.110888234382-0.01293665465410.666453048688-0.0895934878530.389465160565-30.0542372066-41.2198483336-20.9683969082
26.709063584821.323699433622.945618021620.2972494398360.5575494331611.306619699140.0269712403865-1.00413673797-0.108435665473-0.0894585381111-0.2425770815860.100160055226-0.550583949293-1.29226687690.1657221240390.4535410270090.03179985052680.01803968852820.692033710774-0.02905808242240.44203196744-40.7109063567-35.6321961797-12.720217472
32.96701997653-1.591199641251.174650886294.97388749898-0.6607517481453.262833039370.179604394795-0.3380115007880.3440407727050.0227431315284-0.122286440085-0.239318978029-0.1165779629270.1181210956560.02112064830130.415825248965-0.03167991340350.0869343497850.476732025647-0.07472576490010.543456401364-27.3066146182-28.040668043-0.322539135011
42.530101148560.0257743960116-0.2454761402750.1187935546380.2387053109312.490254185440.3328486958860.2006385484380.615917994071-0.177002771875-0.0784904101851-0.0251367963738-0.507356965602-0.191802904008-0.1548332687450.5130242874160.1212625162690.09921012595850.3968990951110.06306427755960.544763623141-46.4897072495-22.8056209382-0.487002353317
52.02057548057-0.387843840051-0.2852498115510.0291558353386-0.1890064978580.7739617917170.0002055695814480.278260517977-0.4426889995880.019001899316-0.05259053874290.06417984510130.029682669557-0.09803170512690.05705731023910.4039441414070.03085382501440.04786034071890.458377554033-0.02206891276690.472177259465-37.2681829993-37.1368199669-7.5022225295
62.206340615940.964306881469-1.115024922310.711629979361-1.084530659022.920853343830.4355577313140.1312851611460.102894904001-0.114521172823-0.338003361558-0.128080015432-0.223610745322-0.04975909437280.03925456189140.5041956573360.1046343679050.01361402371250.4096140681990.006106166719240.399723557869-48.5871538996-27.16687289050.418211370019
73.632529489780.483637457092-3.104395677131.50919650484-1.043779746382.861131475430.4414182689330.3636872447190.612079045815-0.3058130810470.3999192751480.363504209239-0.389953248613-0.454411897616-0.8471777025630.5850452000210.0500218988979-0.02549766786990.4456045229470.06379744163520.60543681744-36.3412015999-24.737456449-6.06279972961
81.29969400976-0.326368002487-0.4612946197521.68335218289-0.09524257946350.4682626528610.1595181106080.1063233954430.0703651201492-0.376869856476-0.03324907192730.3416555905490.597374897534-0.373150499544-0.2424389900520.6423418851960.0283619582137-0.06738435131130.5318246308320.03740351315890.526678272812-38.1588615582-29.6647927978-10.5172884912
94.86827092841.295278383282.293938906554.963762947132.462016172976.24738999768-0.01082091686540.4670524445270.357940733942-0.6146401699560.293497995072-0.411375726732-0.2092708179440.799199934043-0.2867325575920.5033889213370.07082829647090.1460166022340.5777810366680.06211159723840.547699266809-26.2377167613-30.1647189425-15.3951880467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 164 )
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 201 )
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 223 )
9X-RAY DIFFRACTION9chain 'A' and (resid 224 through 241 )

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