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- PDB-5zvh: The crystal structure of NSun6 from Pyrococcus horikoshii with SFG -

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Basic information

Entry
Database: PDB / ID: 5zvh
TitleThe crystal structure of NSun6 from Pyrococcus horikoshii with SFG
Components389aa long hypothetical nucleolar protein
KeywordsRNA BINDING PROTEIN / RNA modification / Archeal / m5C
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 / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Nop2p / 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 / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Nop2p / 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
SINEFUNGIN / tRNA (cytosine(72)-C(5))-methyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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)88,3554
Polymers87,5932
Non-polymers7632
Water2,252125
1
B: 389aa long hypothetical nucleolar protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1782
Polymers43,7961
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 389aa long hypothetical nucleolar protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1782
Polymers43,7961
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.471, 52.941, 84.185
Angle α, β, γ (deg.)81.490, 81.380, 67.450
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-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: magnesium acetate ,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: 2.5→50 Å / Num. obs: 26394 / % possible obs: 92.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.048 / Rrim(I) all: 0.122 / Χ2: 1.008 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.544.40.3279540.9220.1640.3680.80567.1
2.54-2.594.70.32710170.9070.1560.3650.84371.7
2.59-2.644.90.33311520.9340.1530.3690.87178.6
2.64-2.6950.32511540.9210.1480.3590.98883.5
2.69-2.755.10.29112850.9360.1340.3220.86388.3
2.75-2.825.30.27513210.9460.1260.3040.86891.5
2.82-2.895.40.23613420.9570.1080.2610.97294.2
2.89-2.965.50.23613600.9640.1070.260.83995.3
2.96-3.055.60.20613740.9680.0930.2270.95496.4
3.05-3.155.50.19813800.9710.0910.2190.84597
3.15-3.266.20.16914160.9870.0720.1840.8897.7
3.26-3.396.50.15613800.9850.0660.171.04297.4
3.39-3.556.70.14214260.9880.0590.1541.07797.7
3.55-3.736.80.12313800.9930.0510.1330.85898.3
3.73-3.976.70.11314120.990.0470.1231.62398.1
3.97-4.276.50.08814120.9930.0370.0961.59898.7
4.27-4.77.30.08114080.9950.0320.0871.29298.3
4.7-5.387.20.08114140.9940.0320.0870.90798
5.38-6.786.80.08713960.9960.0360.0950.74998.2
6.78-507.10.05614110.9950.0220.060.82698.3

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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: 2.5→41.409 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.13
RfactorNum. reflection% reflection
Rfree0.2295 1285 5.1 %
Rwork0.1822 --
obs0.1846 25193 87.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.06 Å2 / Biso mean: 36.9066 Å2 / Biso min: 16.19 Å2
Refinement stepCycle: final / Resolution: 2.5→41.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 54 125 6335
Biso mean--41.1 37.94 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056334
X-RAY DIFFRACTIONf_angle_d0.9258514
X-RAY DIFFRACTIONf_chiral_restr0.035930
X-RAY DIFFRACTIONf_plane_restr0.0051078
X-RAY DIFFRACTIONf_dihedral_angle_d13.1862480
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3922X-RAY DIFFRACTION2.008TORSIONAL
12B3922X-RAY DIFFRACTION2.008TORSIONAL
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 (%)
2.4932-2.5930.3062950.22021698179357
2.593-2.7110.32021160.23072099221569
2.711-2.85390.27771330.22082469260282
2.8539-3.03260.27431480.22372833298193
3.0326-3.26670.24971560.21782967312397
3.2667-3.59520.22981510.18812922307398
3.5952-4.11510.21511780.16172997317598
4.1151-5.1830.18611570.14972980313798
5.183-41.41430.21381510.16852943309497

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