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- PDB-5zvd: The crystal structure of NSun6 from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 5zvd
TitleThe crystal structure of NSun6 from Pyrococcus horikoshii
Components389aa long hypothetical nucleolar protein
KeywordsRNA BINDING PROTEIN / RNA modification / Archeal / DNA BINDING PROTEIN
Function / homology
Function and homology information


tRNA (cytidine-5-)-methyltransferase activity / RNA methylation / tRNA modification / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding
Similarity search - Function
tRNA (cytosine(72)-C(5))-methyltransferase / : / Methyltr_RsmF/B-like, ferredoxin-like domain / PUA domain / Uncharacterised domain CHP00451 / Nop2p / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase ...tRNA (cytosine(72)-C(5))-methyltransferase / : / Methyltr_RsmF/B-like, ferredoxin-like domain / PUA domain / Uncharacterised domain CHP00451 / Nop2p / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / : / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / PUA domain profile. / PUA-like superfamily / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
tRNA (cytosine(72)-C(5))-methyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsLi, J. / Liu, R.J. / Wang, E.D.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China91440204 China
National Natural Science Foundation of China81471113 China
National Natural Science Foundation of China31770842 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific tRNAs.
Authors: Li, J. / Li, H. / Long, T. / Dong, H. / Wang, E.D. / Liu, R.J.
History
DepositionMay 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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
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: 389aa long hypothetical nucleolar protein
A: 389aa long hypothetical nucleolar protein


Theoretical massNumber of molelcules
Total (without water)87,5932
Polymers87,5932
Non-polymers00
Water1,76598
1
B: 389aa long hypothetical nucleolar protein


Theoretical massNumber of molelcules
Total (without water)43,7961
Polymers43,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 389aa long hypothetical nucleolar protein


Theoretical massNumber of molelcules
Total (without water)43,7961
Polymers43,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.195, 52.605, 83.968
Angle α, β, γ (deg.)81.780, 81.780, 67.930
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 389aa long hypothetical nucleolar protein / NSun6


Mass: 43796.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1991 / Production host: Escherichia coli (E. coli) / References: UniProt: O57712
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: magnesium acetate tetrahydrate,Sodium sodium cacodylate trihydrate , polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.594→50 Å / Num. obs: 23084 / % possible obs: 91.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Χ2: 0.923 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.645.40.3928830.8790.1720.430.96667
2.64-2.695.50.3648960.9090.1560.3971.00273.7
2.69-2.745.70.3239400.930.1380.3530.97874
2.74-2.85.80.31110280.940.1320.3390.96881.3
2.8-2.865.90.26110590.9560.110.2840.97386.2
2.86-2.936.10.25811910.9620.1090.2810.97389.8
2.93-36.30.25311070.9620.1060.2760.98191.2
3-3.086.30.23312400.9620.0980.2530.96795.2
3.08-3.176.30.20911730.9670.0890.2280.99896.6
3.17-3.287.10.18112820.9850.0720.1951.02997
3.28-3.397.30.15511830.9860.0610.1670.95897.5
3.39-3.537.30.13912310.9890.0550.1490.996.4
3.53-3.697.30.1212210.990.0470.130.95797.8
3.69-3.887.20.10312270.9910.0410.1110.90698.1
3.88-4.136.60.08912410.9940.0370.0970.8798.6
4.13-4.457.40.08512520.9920.0330.0910.92298.2
4.45-4.897.50.08112450.9920.0310.0870.88298.3
4.89-5.67.30.08312240.9930.0330.0890.81198.3
5.6-7.056.90.0812390.9920.0320.0860.80597.6
7.05-507.10.06312220.9940.0250.0680.76196.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WWQ

5wwq


Resolution: 2.594→48.14 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.02
RfactorNum. reflection% reflection
Rfree0.2363 1064 4.81 %
Rwork0.1777 --
obs0.1806 22105 87.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.93 Å2 / Biso mean: 39.3567 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: final / Resolution: 2.594→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 0 98 6254
Biso mean---37.55 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056276
X-RAY DIFFRACTIONf_angle_d0.8898430
X-RAY DIFFRACTIONf_chiral_restr0.032918
X-RAY DIFFRACTIONf_plane_restr0.0041074
X-RAY DIFFRACTIONf_dihedral_angle_d13.482478
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5943-2.71240.3215890.2511756184558
2.7124-2.85540.3261940.23712126222071
2.8554-3.03420.33751450.24212570271585
3.0342-3.26850.27191440.23512905304995
3.2685-3.59730.24691480.19632842299097
3.5973-4.11760.24321420.15762974311698
4.1176-5.18670.1771710.13812952312398
5.1867-48.14820.19951310.14842916304797

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