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- PDB-3fyc: Crystal Structure of Dim1 from the thermophilic archeon, Methanoc... -

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Basic information

Entry
Database: PDB / ID: 3fyc
TitleCrystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi
ComponentsProbable dimethyladenosine transferase
KeywordsTRANSFERASE / dimethyladenosine transferase / rossmann fold / rna methylase / ribosomal assembly / Methyltransferase / RNA-binding / rRNA processing / S-adenosyl-L-methionine
Function / homology
Function and homology information


rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / cytoplasm
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsScarsdale, J.N. / Musayev, F.N. / Rife, J.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.
Authors: Pulicherla, N. / Pogorzala, L.A. / Xu, Z. / O Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / Sia, E.A. / Culver, G.M. / Rife, J.P.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Probable dimethyladenosine transferase
B: Probable dimethyladenosine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,00411
Polymers61,1492
Non-polymers8559
Water5,134285
1
A: Probable dimethyladenosine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9545
Polymers30,5741
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable dimethyladenosine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0496
Polymers30,5741
Non-polymers4755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.384, 72.274, 95.883
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable dimethyladenosine transferase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase / 16S rRNA dimethylase


Mass: 30574.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: ksgA, MJ1029 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q58435, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 3350 (18%), 25 mM MES, 50 mM Na2HPO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 23, 2008 / Details: Rigaku Varimax confocal optics
RadiationMonochromator: Rigaku Varimax Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→32.77 Å / Num. all: 30159 / Num. obs: 28619 / % possible obs: 94.9 % / Redundancy: 6.62 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.4
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.65 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.7 / Num. unique all: 3014 / % possible all: 91.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9

1qyr

2h1r

1zq9


Resolution: 2.15→32 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.244 / SU ML: 0.205
Isotropic thermal model: TLS for each domain in a monomer with individual residual isotropic B-factors for each atom
Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27332 2873 10 %RANDOM
Rwork0.20237 ---
obs0.20946 25730 94.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.407 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å2-1.33 Å2
2--3.05 Å20 Å2
3----0.88 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: LAST / Resolution: 2.15→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 50 292 4649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.985990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08425.369203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1151517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023271
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.22097
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23092
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.82322766
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6854354
X-RAY DIFFRACTIONr_scbond_it2.69261856
X-RAY DIFFRACTIONr_scangle_it4.13591636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 203 -
Rwork0.309 1840 -
obs--91.82 %

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