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- PDB-6l7w: Crystal structure of Cet1 from Trypanosoma cruzi in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6l7w
TitleCrystal structure of Cet1 from Trypanosoma cruzi in complex with manganese ion.
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
: / mRNA 5'-phosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi strain CL Brener (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA_triPase domain-containing protein
B: mRNA_triPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7044
Polymers47,5942
Non-polymers1102
Water73941
1
A: mRNA_triPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8522
Polymers23,7971
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-5 kcal/mol
Surface area9670 Å2
MethodPISA
2
B: mRNA_triPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8522
Polymers23,7971
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-4 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.445, 73.208, 63.747
Angle α, β, γ (deg.)90.000, 114.063, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein mRNA_triPase domain-containing protein


Mass: 23797.006 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES-NaOH, PEG 20000 / PH range: 7.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→47.89 Å / Num. obs: 13646 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 43.15 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.142 / Net I/σ(I): 9.9
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1652 / CC1/2: 0.709 / Rrim(I) all: 1.003 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1300014194

Resolution: 2.6→47.89 Å / SU ML: 0.3543 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.6058 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2941 632 4.64 %
Rwork0.2388 12983 -
obs0.2414 13615 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.98 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 2 41 2893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362894
X-RAY DIFFRACTIONf_angle_d0.57033911
X-RAY DIFFRACTIONf_chiral_restr0.0426459
X-RAY DIFFRACTIONf_plane_restr0.003496
X-RAY DIFFRACTIONf_dihedral_angle_d8.98891743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.40381270.32982584X-RAY DIFFRACTION99.82
2.8-3.080.3631300.30732575X-RAY DIFFRACTION99.96
3.08-3.530.29571250.26032594X-RAY DIFFRACTION99.67
3.53-4.450.2441210.2112606X-RAY DIFFRACTION99.85
4.45-47.890.27881290.20232624X-RAY DIFFRACTION99.24
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)
15.007407688073.18330103262-0.9120488441991.99852267374-0.1455592540379.027135931260.0218495194679-1.626383458180.129503915940.838221131136-0.1315803186130.4509294000040.493693458635-0.924066538005-0.1739937522220.4304273937880.09174821888610.06840094629520.6686292755120.009429264770480.479579094551-13.8129240801-11.97450303419.31778171195
25.24288337764-3.521634647881.476979200512.45677982074-0.1661306634362.2146640127-0.549918560054-0.7656897572910.1640383324710.4837884175740.595604441389-0.41084099071-0.3144251262080.0184055825114-0.03342470460140.5719119426330.0760314886957-0.01032974864890.322981942574-0.02055014437460.4302816407831.32579768808-12.0503499648.50075621498
32.285783209750.838890418106-1.810302484493.987286716890.08593417804393.06392556770.0489825846569-0.1238646374920.03379437992890.260085013140.0259942653184-0.506772803548-0.1570410512640.3123808918320.02148086655420.3078404832080.0259127218265-0.04760359503280.361624615810.0126070403190.34723442894310.0935912467-11.77925480341.11739713938
40.185612521143-1.09380756422-0.6988469482413.22223934192-0.2605892565713.122071215880.01399282665110.06186050032690.1145143566450.0917827656624-0.123350176619-0.26384717103-0.1077312620060.0524885953050.2269394700450.41036869211-0.008023141227520.03513096323780.282402902818-0.01105430030380.4112920451384.60949825432-13.55664118686.26874959468
58.32355060167-1.636681030044.185019390954.1158101545-0.3473362513966.905563449230.01663219984680.2100077579380.02877889660880.119117011094-0.0133381841492-0.527778314356-0.04878750118610.5650238494870.1997342301040.358922492604-0.01448414774790.02289974434730.3240413610340.04138066298140.302666785198.15634241637-15.64920277193.12965477903
68.72684070927-3.335001606720.9255770402554.09100645049-1.5934695215.82888594728-0.0147922896088-0.2006237774250.00843475398858-0.09892823533620.03353098110820.082727847317-0.0817939335983-0.722040261621-0.09681445640770.381173031156-0.0462555484886-0.001534330334780.360114451914-0.03651960294820.265747831877-7.1514347301-15.85383693171.57372253759
76.24093170730.1455153242160.5167618628074.936323248321.373252045585.11343339171-0.0243735094468-0.6656942661780.9130455352330.1831392246940.5023244380711.14189817919-1.55133746710.511964624401-0.05723585833610.6000602562790.06908305107310.06070036142810.494932637621-0.07577836036180.424692159519-9.77270572539-17.465113770146.0756352561
81.91021893860.376094967625-1.675491862692.782892499850.4355416589443.25736298149-0.1108869831260.390072808921-0.171940173687-0.2607769815950.041077069230.2186456186860.129279047441-0.4587776975440.06594084551190.3337495604330.0066086218678-0.01400742789230.351219455056-0.02815087824380.34566288577-19.0276991211-19.009145376726.8940793864
91.58488703948-0.01828043351141.23695562744.789300027013.230343574387.06194559350.007753067496610.269063002792-0.451479826382-0.509917507879-0.3385045773320.405457542635-0.0569970055067-1.235408267430.2045172563710.6839822122420.06477947594230.09914548866140.417372777706-0.0853271729580.508394096329-23.7482080224-26.984086384624.0407928022
103.17559025919-3.114050605250.1454544671847.64514315968-2.225281205182.591231817540.3762527607410.572738589037-0.0741308727523-0.698846595712-0.66638314674-0.372722683897-0.0855828250777-0.2822525502290.2275697478740.438242759728-0.09168087192870.129802307960.380079469151-0.01096100487060.3114191202-20.2438260375-16.465738223437.271846417
112.398404589030.05748018622910.515342180943.772884904141.369487318331.00328282776-0.01570845207210.0267859941625-0.304797012469-0.308800714969-0.0737827095771-0.03286565349580.0117646411601-0.2728745005670.08122340362650.4169855578140.02200169719880.1256382708360.417363042024-0.01849410378980.311307077209-16.9389369704-19.302262504825.6028118081
123.51771868963-1.941957824441.606299962554.83347096951-1.458799446465.469242146920.167809008511-0.300003735838-0.0228271946243-0.477547066356-0.136077623322-0.153480561459-0.7889225725270.1578195246790.2720080575740.450967097168-0.08067085011420.06274750178750.360178696107-0.05716725101880.307274894354-11.3705641341-11.257755135636.0374232377
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 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 146 )
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 189 )
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 242 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 122 )
9X-RAY DIFFRACTION9chain 'B' and (resid 123 through 146 )
10X-RAY DIFFRACTION10chain 'B' and (resid 147 through 163 )
11X-RAY DIFFRACTION11chain 'B' and (resid 164 through 223 )
12X-RAY DIFFRACTION12chain 'B' and (resid 224 through 242 )

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