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- PDB-3jwi: Crystal structure analysis of the methyltransferase domain of bac... -

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Basic information

Entry
Database: PDB / ID: 3jwi
TitleCrystal structure analysis of the methyltransferase domain of bacterial-CtHen1-CN
ComponentsMethyltransferase type 12
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


small RNA 2'-O-methyltransferase / RNA methyltransferase activity / RNA methylation / regulatory ncRNA-mediated gene silencing / O-methyltransferase activity / identical protein binding / metal ion binding
Similarity search - Function
3'-RNA ribose 2'-O-methyltransferase, Hen1, bacterial / Hen1, N-terminal / Hen1, N-terminal domain superfamily / RNA repair, ligase-Pnkp-associating, region of Hen1 / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / Methyltransferase type 12 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...3'-RNA ribose 2'-O-methyltransferase, Hen1, bacterial / Hen1, N-terminal / Hen1, N-terminal domain superfamily / RNA repair, ligase-Pnkp-associating, region of Hen1 / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / Methyltransferase type 12 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small RNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuang, R.H. / Chan, C.M. / Zhou, C. / Brunzelle, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and biochemical insights into 2'-O-methylation at the 3'-terminal nucleotide of RNA by Hen1.
Authors: Mui Chan, C. / Zhou, C. / Brunzelle, J.S. / Huang, R.H.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Methyltransferase type 12
B: Methyltransferase type 12


Theoretical massNumber of molelcules
Total (without water)48,4452
Polymers48,4452
Non-polymers00
Water2,576143
1
A: Methyltransferase type 12


Theoretical massNumber of molelcules
Total (without water)24,2231
Polymers24,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyltransferase type 12


Theoretical massNumber of molelcules
Total (without water)24,2231
Polymers24,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.456, 82.228, 88.053
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,B, using restrain
22chain A,B, using restrain

NCS ensembles :
ID
1
2

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Components

#1: Protein Methyltransferase type 12 / Hen1


Mass: 24222.543 Da / Num. of mol.: 2 / Fragment: UNP residues 259-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2767 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DJ37
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: PEG 6000, pH 5.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorDetector: CCD / Date: Aug 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25408

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.847 / σ(F): 1397
RfactorNum. reflection% reflection
Rfree0.249 1800 7.1 %
Rwork0.204 --
obs-22933 89.9 %
Solvent computationBsol: 46.21 Å2
Displacement parametersBiso max: 76.77 Å2 / Biso mean: 31.133 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1--12.486 Å20 Å20 Å2
2---9.223 Å20 Å2
3---21.709 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 143 3310
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.118
X-RAY DIFFRACTIONc_mcbond_it1.3911.5
X-RAY DIFFRACTIONc_scbond_it2.2862
X-RAY DIFFRACTIONc_mcangle_it2.2152
X-RAY DIFFRACTIONc_scangle_it3.3982.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0restrain200
22BX-RAY DIFFRACTION0restrain200
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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