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- PDB-6l7v: Crystal structure of Cet1 from Trypanosoma cruzi in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6l7v
TitleCrystal structure of Cet1 from Trypanosoma cruzi in complex with tripolyphosphate, manganese and iodide ions.
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
TRIPHOSPHATE / IODIDE ION / : / mRNA 5'-phosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA_triPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,99810
Polymers23,7971
Non-polymers1,2019
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-12 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.266, 67.266, 76.820
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium acetate (pH 5.0), 1,4-butandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.2→46.42 Å / Num. obs: 21226 / % possible obs: 100 % / Redundancy: 38.6 % / Biso Wilson estimate: 42.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.096 / Net I/σ(I): 33.5
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 5.854 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1814 / CC1/2: 0.955 / Rrim(I) all: 5.939

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→46.42 Å / SU ML: 0.3444 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 33.2355
RfactorNum. reflection% reflection
Rfree0.2607 948 4.89 %
Rwork0.2238 --
obs0.2256 19373 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 21 26 1449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321434
X-RAY DIFFRACTIONf_angle_d0.6191944
X-RAY DIFFRACTIONf_chiral_restr0.0448229
X-RAY DIFFRACTIONf_plane_restr0.0037244
X-RAY DIFFRACTIONf_dihedral_angle_d11.9593858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.320.46711180.41222355X-RAY DIFFRACTION86.62
2.32-2.460.28841180.25642669X-RAY DIFFRACTION100
2.46-2.650.31841280.25962687X-RAY DIFFRACTION100
2.65-2.920.25571520.24752701X-RAY DIFFRACTION100
2.92-3.340.28141180.21742699X-RAY DIFFRACTION100
3.34-4.210.22231740.20562638X-RAY DIFFRACTION99.89
4.21-46.420.25351400.19852676X-RAY DIFFRACTION100
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)
18.924299707851.803315385132.359805820784.569427968830.711890227369.00212266030.0976257144876-0.1007958716920.3398859768450.14781784412-0.09150317588870.504587386977-0.6548175301380.312366166149-0.2177577567010.427881382062-0.01482563364210.08428682529850.3526066708060.002102119293330.362506223351-30.662883489915.3564129266-22.1190508558
22.5138514822-1.204819027261.471863913754.840816388422.587408461818.259244071060.2935666927260.209887822618-0.666525381133-0.396910941861-0.1497860453190.7626286915930.805855628678-1.15287727432-0.1563941011820.42975010361-0.0749047431103-0.05610812547640.618442389426-0.03273705400740.483582807705-8.9121175534221.8526173711-0.187066622894
32.200010468971.754143137880.07958409261516.10450106323.261496886637.914737123250.08211864800760.0222897732392-1.48551820966-0.7214947671040.411274471242-0.604154087621.011549971361.34338694618-0.5268586204460.5767303309330.106597834924-0.01968067621360.496217269624-0.06162716411310.6365920481765.3934812563617.770105118212.8430336207
48.9432829219-7.223531954090.5102769588533.326278750292.116555316188.99567010082-0.355229103221-0.613096392109-0.1825650995070.7565611360960.448815397520.09093489034720.477103203902-0.203779864993-0.04075206978290.332971804537-0.0667533310027-0.01370649513150.36053907632-0.008990718205760.326213977146-6.4123570527828.097232465821.9571615374
53.881854148680.539480254687-0.184414769176.3852899276-0.8493313759664.71209165621-0.466271540150.538234010856-0.768519780561-0.6366451630890.742515202507-0.1403418575621.03356949544-0.495563492045-0.3639647499090.516445086717-0.227254170873-0.007141825911180.659918009821-0.05252561487920.533018133089-18.373969610514.171912116812.8908240225
61.347501859610.188679763722-0.627344782431.39747624381-1.31954234715.3509427574-0.1723154289470.0870092439548-0.376780410718-0.379837657696-0.1169637113380.1852464077860.756115072657-0.6433821769580.3391665656820.3700077346560.01150069141120.02437342956270.478940376251-0.1133535366050.510075492609-1.7545161616620.89076366433.9684759212
78.842860468544.871004076517.501109781538.62387713614.685779052933.591700773220.136093735428-0.82751795058-0.572319299836-0.269425354428-0.3699490115290.2704261940661.18295277456-1.477820903250.261829552380.492179948248-0.0827671863365-0.01244461801670.565009317307-0.0499064477940.340349945829-3.1810031499121.34084466241.10796614061
86.010463008480.949634737441-1.096341341015.7360600915-1.90237929097.332102190020.06524649426560.41232869327-0.547357813106-0.3190578953330.04685023236250.03581109929430.702227017627-0.288955517737-0.09964123335850.301912477294-0.0212672759773-0.00265870547030.372192198256-0.07157670993990.383213029106-9.9830157257621.61426845379.67477263948
910.3462164089-0.8357485618923.080382564012.07277833323-0.6987894081588.996382561170.06113325221230.1286854876140.223178043931-0.061011401557-0.192060198076-0.233235872492-0.483441063162-0.3086909431680.1051732571420.29121163350.04839463702370.05390484330570.331077686077-0.02127117032560.425631182123-1.6665529859334.30638743039.07772747906
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 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 153 )
7X-RAY DIFFRACTION7chain 'A' and (resid 154 through 163 )
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 223 )
9X-RAY DIFFRACTION9chain 'A' and (resid 224 through 242 )

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