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- PDB-5wwq: Crystal structure of human NSun6 -

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Basic information

Entry
Database: PDB / ID: 5wwq
TitleCrystal structure of human NSun6
ComponentsPutative methyltransferase NSUN6
KeywordsTRANSFERASE / RNA modification / m5C methyltransferase / NSun
Function / homology
Function and homology information


tRNA C5-cytosine methylation / tRNA (cytidine-5-)-methyltransferase activity / tRNA modification in the nucleus and cytosol / tRNA modification / RNA methylation / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / cytosol / cytoplasm
Similarity search - Function
Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / PUA domain profile. / PUA domain superfamily / PUA-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.815 Å
AuthorsLiu, R.J. / Long, T. / Wang, E.D.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270775 China
National Natural Science Foundation of China81471113 China
National Natural Science Foundation of China91440204 China
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6
Authors: Liu, R.J. / Long, T. / Li, J. / Li, H. / Wang, E.D.
History
DepositionJan 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyltransferase NSUN6
B: Putative methyltransferase NSUN6


Theoretical massNumber of molelcules
Total (without water)105,8102
Polymers105,8102
Non-polymers00
Water0
1
A: Putative methyltransferase NSUN6


Theoretical massNumber of molelcules
Total (without water)52,9051
Polymers52,9051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative methyltransferase NSUN6


Theoretical massNumber of molelcules
Total (without water)52,9051
Polymers52,9051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.965, 71.877, 219.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRchain AAA2 - 4692 - 469
2CYSCYSchain BBB2 - 4662 - 466

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Components

#1: Protein Putative methyltransferase NSUN6 / NOL1/NOP2/Sun and PUA domain-containing protein 1 / NOL1/NOP2/Sun domain family member 6


Mass: 52905.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSUN6, NOPD1
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q8TEA1, Transferases; Transferring one-carbon groups; Methyltransferases

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.6
Details: 2% Dioxane, 0.1M Bicine, 18% (w/v) PEG 8000, 10 mM Yttrium(III) chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 26419 / % possible obs: 97.6 % / Redundancy: 24.5 % / Net I/σ(I): 15.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
SCALEPACKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2B, 2yxl

1j2b

2yxl


Resolution: 2.815→37.406 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.95
RfactorNum. reflection% reflection
Rfree0.2667 1207 5.12 %
Rwork0.2285 --
obs0.2303 23578 89.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.41 Å2 / Biso mean: 54.2703 Å2 / Biso min: 19.15 Å2
Refinement stepCycle: final / Resolution: 2.815→37.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6846 0 0 0 6846
Num. residues----887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026980
X-RAY DIFFRACTIONf_angle_d0.6569431
X-RAY DIFFRACTIONf_chiral_restr0.0231080
X-RAY DIFFRACTIONf_plane_restr0.0031215
X-RAY DIFFRACTIONf_dihedral_angle_d11.6112647
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4072X-RAY DIFFRACTION7.245TORSIONAL
12B4072X-RAY DIFFRACTION7.245TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8153-2.9280.2993810.27231679176061
2.928-3.06120.35391100.27211947205771
3.0612-3.22250.31441200.26832186230680
3.2225-3.42430.2871410.26272467260890
3.4243-3.68850.3091590.24652720287999
3.6885-4.05920.2611350.234627792914100
4.0592-4.64570.22791540.193827882942100
4.6457-5.84950.25081470.209728342981100
5.8495-37.40960.24061600.213929713131100
Refinement TLS params.Method: refined / Origin x: 54.3381 Å / Origin y: 33.7716 Å / Origin z: 135.1311 Å
111213212223313233
T0.334 Å20.0429 Å2-0.0509 Å2-0.2671 Å20.0149 Å2--0.3451 Å2
L0.3847 °20.171 °20.2355 °2-0.5115 °20.2473 °2--2.0084 °2
S-0.0398 Å °-0.0119 Å °0.1326 Å °0.2423 Å °-0.0385 Å °-0.0238 Å °-0.3847 Å °-0.1427 Å °0.0704 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 469
2X-RAY DIFFRACTION1allB2 - 466

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