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- PDB-5zve: The crystal structure of NSun6 from Pyrococcus horikoshii with SAH -

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Basic information

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


tRNA (cytidine-5-)-methyltransferase activity / tRNA modification / RNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding
Similarity search - Function
tRNA (cytosine(72)-C(5))-methyltransferase / Uncharacterised domain CHP00451 / PUA domain / 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 ...tRNA (cytosine(72)-C(5))-methyltransferase / Uncharacterised domain CHP00451 / PUA domain / 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 profile. / PUA domain superfamily / PUA-like superfamily / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / tRNA (cytosine(72)-C(5))-methyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.178 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 / 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

Downloads & links

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Assembly

Deposited unit
B: 389aa long hypothetical nucleolar protein
A: 389aa long hypothetical nucleolar protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3614
Polymers87,5932
Non-polymers7692
Water5,819323
1
B: 389aa long hypothetical nucleolar protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1812
Polymers43,7961
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 389aa long hypothetical nucleolar protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1812
Polymers43,7961
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.982, 52.176, 83.804
Angle α, β, γ (deg.)80.630, 80.580, 67.900
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 5 - 388 / Label seq-ID: 1 - 384

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBA

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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: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.178→50 Å / Num. obs: 39682 / % possible obs: 93.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 27.31 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.054 / Rrim(I) all: 0.144 / Χ2: 2.062 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.18-2.224.60.42115430.9130.1990.4680.45273.8
2.22-2.264.90.41317120.9390.1880.4550.72779.5
2.26-2.35.20.46617670.9180.2090.5130.59683.6
2.3-2.355.40.42718440.9270.1880.4680.65786.7
2.35-2.45.60.40619270.9390.1760.4440.57490.4
2.4-2.465.90.3719480.9560.1570.4030.77292.2
2.46-2.525.90.36320370.9580.1560.3960.68395.4
2.52-2.586.20.32320200.960.1380.3520.67395.6
2.58-2.6670.32620890.9650.130.3510.75697.4
2.66-2.757.20.29220610.9510.1160.3151.00197.2
2.75-2.847.20.23720380.9760.0940.2560.92696.8
2.84-2.967.10.220800.9870.080.2160.79697.1
2.96-3.096.70.17220840.9850.0710.1861.31896.9
3.09-3.267.10.14120630.9920.0570.1521.22697.6
3.26-3.467.40.11520440.9950.0450.1241.45497
3.46-3.737.30.09820890.9860.0380.1052.47997.9
3.73-4.16.80.08220890.9920.0330.0883.1298.3
4.1-4.77.30.07520720.9950.030.0814.3298.1
4.7-5.917.10.08921020.9710.0350.0954.62798
5.91-507.30.10920730.9780.0420.1179.78297.9

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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: 2.178→41.082 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 27.04
RfactorNum. reflection% reflection
Rfree0.2361 1997 5.05 %
Rwork0.1891 --
obs0.1914 39519 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.61 Å2 / Biso mean: 31.7954 Å2 / Biso min: 15.33 Å2
Refinement stepCycle: final / Resolution: 2.178→41.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 52 323 6531
Biso mean--30.4 35.04 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046332
X-RAY DIFFRACTIONf_angle_d0.9018510
X-RAY DIFFRACTIONf_chiral_restr0.035928
X-RAY DIFFRACTIONf_plane_restr0.0041078
X-RAY DIFFRACTIONf_dihedral_angle_d13.1682506
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3920X-RAY DIFFRACTION4.459TORSIONAL
12B3920X-RAY DIFFRACTION4.459TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1776-2.23210.28771030.22652039214271
2.2321-2.29240.33731220.2282385250782
2.2924-2.35990.29051400.2312512265287
2.3599-2.4360.29091480.22922625277391
2.436-2.52310.28561470.23072744289195
2.5231-2.62410.27671470.22172791293896
2.6241-2.74350.23391520.21962804295697
2.7435-2.88810.25071490.20842787293697
2.8881-3.0690.2671370.22042841297897
3.069-3.30580.29081630.21462803296698
3.3058-3.63830.23691540.18432807296197
3.6383-4.16440.19271460.15972829297598
4.1644-5.2450.18411370.14352838297597
5.245-41.08920.19151520.16222717286994

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