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- PDB-3id6: Crystal structure of Sulfolobus solfataricus Nop5 (1-262) and fib... -

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Basic information

Entry
Database: PDB / ID: 3id6
TitleCrystal structure of Sulfolobus solfataricus Nop5 (1-262) and fibrillarin complex
Components
  • Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
  • Pre mRNA splicing protein
KeywordsTRANSFERASE / C/D guide RNA / 2'-O-methylation / coiled-coil / Methyltransferase / RNA-binding / rRNA processing / tRNA processing
Function / homology
Function and homology information


histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / : / Archaeal Nop5/56-rel, N-terminal domain / : / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. ...Nucleotidyltransferase; domain 5 - #220 / Helix Hairpins - #4070 / : / Archaeal Nop5/56-rel, N-terminal domain / : / Nucleolar protein Nop56/Nop58 / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Vaccinia Virus protein VP39 / Nucleotidyltransferase; domain 5 / Helix Hairpins / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / Pre mRNA splicing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYe, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural organization of box C/D RNA-guided RNA methyltransferase.
Authors: Ye, K. / Jia, R. / Lin, J. / Ju, M. / Peng, J. / Xu, A. / Zhang, L.
History
DepositionJul 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre mRNA splicing protein
C: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9743
Polymers57,5762
Non-polymers3981
Water00
1
A: Pre mRNA splicing protein
C: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules

A: Pre mRNA splicing protein
C: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9486
Polymers115,1514
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8630 Å2
ΔGint-53 kcal/mol
Surface area43800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.517, 182.364, 79.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Pre mRNA splicing protein / Nop5


Mass: 31136.340 Da / Num. of mol.: 1 / Fragment: NTD and coiled-coil domain (residues 1-262) / Mutation: M2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0939 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+ / References: UniProt: Q97ZH3
#2: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / fibrillarin / FIB


Mass: 26439.375 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: flpA, SSO0940, C33_014 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+
References: UniProt: P58032, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 3350, 0.2M KF, pH 7.2, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22817 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NNW

2nnw


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 28.236 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.509 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 876 5.1 %RANDOM
Rwork0.232 ---
obs0.235 17155 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.15 Å2 / Biso mean: 32.101 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2--0.09 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 27 0 3908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223977
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9815375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92124.416197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.61915732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8891529
X-RAY DIFFRACTIONr_chiral_restr0.0960.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022977
X-RAY DIFFRACTIONr_nbd_refined0.2130.21645
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.24
X-RAY DIFFRACTIONr_mcbond_it0.4051.52455
X-RAY DIFFRACTIONr_mcangle_it0.70323871
X-RAY DIFFRACTIONr_scbond_it1.06431715
X-RAY DIFFRACTIONr_scangle_it1.7334.51504
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 68 -
Rwork0.286 1158 -
all-1226 -
obs--99.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.6966-8.04881.996116.018-3.07879.6687-0.4158-0.8023-0.75921.20770.3642-0.12160.841-0.03230.05170.2577-0.0310.0896-0.02650.08710.2159-18.892-47.824-28.162
27.2332-4.43981.57646.3703-2.0646.0488-0.5521-0.8627-0.42860.88460.6960.74970.0074-0.6966-0.14390.1981-0.02940.23920.00270.08860.1238-26.108-43.608-23.383
33.5053-1.85511.63447.1329-1.09896.04410.24280.3563-0.2849-0.1387-0.4780.08930.39370.13340.23520.0466-0.09140.07030.0474-0.0620.2196-21.888-40.046-38.513
40.7937-0.0793-0.15514.71794.31244.83880.04330.11070.0625-0.4497-0.20340.3218-0.4189-0.22830.16010.20230.02510.01580.09330.04020.1687-31.7633.248-7.276
51.1479-0.0095-0.94954.79461.16574.12130.11670.00530.1496-0.3410.0777-0.2157-0.70620.343-0.19440.1374-0.05790.05770.11380.01040.2255-23.82815.415-1.304
64.66631.40111.0336.5287-3.419810.2147-0.22530.37360.5337-0.5157-0.2407-0.3279-1.51860.55850.4660.3722-0.1254-0.0495-0.03690.0630.0405-11.677-14.667-55.478
74.49760.42120.30664.2531-0.40695.887-0.008-0.2806-0.0260.2176-0.2359-0.1214-0.45260.06430.24390.0848-0.0803-0.06770.0379-0.01340.1465-15.353-25.193-37.569
810.59683.01433.90176.2426-1.94344.6553-0.3318-0.30930.1001-0.0339-0.0047-0.2829-0.93470.71580.33650.0331-0.2952-0.15090.4640.15340.23915.26-19.117-34.375
9120.372842.4403143.624107.7208-26.3865235.32670.40371.51724.97421.650.03614.5725-1.7137.83-0.43980.3164-0.0658-0.00880.33250.12750.5285-3.851-8.603-38.758
108.48695.39395.30698.65851.16454.2509-0.5155-0.0121-0.32021.89010.5125-0.52470.37091.29120.00290.3592-0.18910.06350.3880.09550.35080.098-27.323-37.312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 20
2X-RAY DIFFRACTION2A21 - 83
3X-RAY DIFFRACTION3A84 - 123
4X-RAY DIFFRACTION4A124 - 188
5X-RAY DIFFRACTION5A189 - 259
6X-RAY DIFFRACTION6C5 - 72
7X-RAY DIFFRACTION7C73 - 180
8X-RAY DIFFRACTION8C181 - 218
9X-RAY DIFFRACTION9C219 - 223
10X-RAY DIFFRACTION10C224 - 231

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