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- PDB-6zd3: Crystal structure of YTHDC1 M438A mutant -

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Basic information

Entry
Database: PDB / ID: 6zd3
TitleCrystal structure of YTHDC1 M438A mutant
ComponentsYTH domain containing 1
KeywordsRNA BINDING PROTEIN / YTHDC1 / m6A / complex / inhibitor
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBedi, R.K. / Li, Y. / Caflisch, A.
Funding support Switzerland, Sweden, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_189363 Switzerland
Swedish Research CouncilVR 2019-00608 Sweden
CitationJournal: J Chem Theory Comput / Year: 2021
Title: Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1.
Authors: Li, Y. / Bedi, R.K. / Wiedmer, L. / Sun, X. / Huang, D. / Caflisch, A.
History
DepositionJun 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
B: YTH domain containing 1
A: YTH domain containing 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,60310
Polymers41,8142
Non-polymers7898
Water9,908550
1
B: YTH domain containing 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6008
Polymers20,9071
Non-polymers6937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: YTH domain containing 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0032
Polymers20,9071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.710, 103.130, 42.310
Angle α, β, γ (deg.)90.000, 105.422, 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 YTH domain containing 1


Mass: 20907.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YTHDC1 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2M Ammonium Sulphate, 0.1M bis-tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→40.79 Å / Num. obs: 88036 / % possible obs: 97.3 % / Redundancy: 4.55 % / Biso Wilson estimate: 13.97 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.71
Reflection shellResolution: 1.25→1.33 Å / Num. unique obs: 13842 / CC1/2: 0.519

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3h

4r3h


Resolution: 1.25→40.79 Å / SU ML: 0.1698 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 4390 5 %
Rwork0.1921 83362 -
obs0.1931 87752 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.04 Å2
Refinement stepCycle: LAST / Resolution: 1.25→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 44 550 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562692
X-RAY DIFFRACTIONf_angle_d0.80993675
X-RAY DIFFRACTIONf_chiral_restr0.0826403
X-RAY DIFFRACTIONf_plane_restr0.0049463
X-RAY DIFFRACTIONf_dihedral_angle_d14.6303378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.39181350.3592568X-RAY DIFFRACTION90.07
1.26-1.280.35991440.34922730X-RAY DIFFRACTION93.65
1.28-1.290.33571380.32992640X-RAY DIFFRACTION95.27
1.29-1.310.39481450.32532742X-RAY DIFFRACTION94.97
1.31-1.330.32061430.31512712X-RAY DIFFRACTION94.69
1.33-1.350.29731440.30752736X-RAY DIFFRACTION95.62
1.35-1.370.31881430.28892728X-RAY DIFFRACTION95.48
1.37-1.390.28211440.28062719X-RAY DIFFRACTION95.88
1.39-1.410.32741430.27272733X-RAY DIFFRACTION95.74
1.41-1.430.31081450.26782748X-RAY DIFFRACTION96.11
1.43-1.460.28881450.26752759X-RAY DIFFRACTION96.74
1.46-1.480.25571460.24692760X-RAY DIFFRACTION96.54
1.48-1.510.28841470.23362793X-RAY DIFFRACTION97.25
1.51-1.540.25811430.21752725X-RAY DIFFRACTION96.73
1.54-1.570.22911470.20492798X-RAY DIFFRACTION97.36
1.57-1.610.2331480.19622798X-RAY DIFFRACTION97.61
1.61-1.650.20961480.19762808X-RAY DIFFRACTION97.69
1.65-1.70.2161470.19062788X-RAY DIFFRACTION97.9
1.7-1.750.21821460.19852786X-RAY DIFFRACTION97.99
1.75-1.80.21671490.19282834X-RAY DIFFRACTION98.25
1.8-1.870.22531480.19612814X-RAY DIFFRACTION98.77
1.87-1.940.21741490.18632817X-RAY DIFFRACTION98.54
1.94-2.030.21381490.18092829X-RAY DIFFRACTION98.84
2.03-2.140.22021490.1742840X-RAY DIFFRACTION98.81
2.14-2.270.20871500.17332840X-RAY DIFFRACTION99.17
2.27-2.450.20241490.17852839X-RAY DIFFRACTION99.07
2.45-2.690.21411500.18112846X-RAY DIFFRACTION99.21
2.69-3.080.21221510.18282873X-RAY DIFFRACTION99.51
3.08-3.880.16061510.15682857X-RAY DIFFRACTION99.37
3.88-40.790.15771540.16232902X-RAY DIFFRACTION99.35

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