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

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Basic information

Entry
Database: PDB / ID: 3jwh
TitleCrystal structure analysis of the methyltransferase domain of bacterial-AvHen1-C
ComponentsHen1
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
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 domain / 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 domain / 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
S-ADENOSYL-L-HOMOCYSTEINE / Small RNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hen1
B: Hen1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1384
Polymers50,3692
Non-polymers7692
Water1,35175
1
A: Hen1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5692
Polymers25,1851
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hen1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5692
Polymers25,1851
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.519, 49.772, 90.433
Angle α, β, γ (deg.)90.000, 101.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hen1


Mass: 25184.617 Da / Num. of mol.: 2 / Fragment: unp residues 253-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / PCC 7937 / Gene: Ava_1594 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3MCR9
#2: Chemical ChemComp-SAH / 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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 6000, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorDetector: CCD
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: 24150

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.772 / σ(F): 1034
RfactorNum. reflection% reflection
Rfree0.291 1769 7 %
Rwork0.236 --
obs-22455 88.6 %
Solvent computationBsol: 34.911 Å2
Displacement parametersBiso max: 92.16 Å2 / Biso mean: 39.805 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1-22.402 Å20 Å25.038 Å2
2---9.263 Å20 Å2
3----13.139 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 52 75 3188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.184
X-RAY DIFFRACTIONc_mcbond_it1.5151.5
X-RAY DIFFRACTIONc_scbond_it2.0742
X-RAY DIFFRACTIONc_mcangle_it2.4742
X-RAY DIFFRACTIONc_scangle_it3.1712.5
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
X-RAY DIFFRACTION5SAH1.parSAH1.top

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