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- PDB-3grr: Crystal Structure of the complex between S-Adenosyl Homocysteine ... -

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Basic information

Entry
Database: PDB / ID: 3grr
TitleCrystal Structure of the complex between S-Adenosyl Homocysteine and Methanocaldococcus jannaschi Dim1.
ComponentsDimethyladenosine transferase
KeywordsTRANSFERASE / DimethylAdenosine Transferase / Rossmann fold / Ribosomal Assembly S-Adenosyl-L-Methionine / RRNA Processing / RNA-Binding / Methyl Transferase / Methyltransferase / 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
S-ADENOSYL-L-HOMOCYSTEINE / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsScarsdale, J.N. / Musayev, F.N. / Rife, J.P.
Citation
Journal: Biochemistry / Year: 2010
Title: Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design.
Authors: O'Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / Rife, J.P.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli
Authors: O'Farrell, H.C. / Scarsdale, J.N. / Rife, J.P.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 20, 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 1.4Sep 6, 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: Dimethyladenosine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2622
Polymers33,8771
Non-polymers3841
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.385, 66.299, 62.061
Angle α, β, γ (deg.)90.00, 107.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33877.305 Da / Num. of mol.: 1 / Mutation: K137A,E138A
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000 (14-16%), 25 MM MES, 50 MM NH2SO4, 7 MM MGCL2, 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: Jun 8, 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: 1.8→17.7 Å / Num. all: 28976 / Num. obs: 27022 / % possible obs: 93.3 % / Redundancy: 4.59 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 18.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.45 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4 / Num. unique all: 2880 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FYD, chain A

3fyd


Resolution: 1.8→17.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.735 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Residual Isotropic B factors with TLS refinement
Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23377 2733 10.1 %RANDOM
Rwork0.18218 ---
obs0.18732 24273 93.25 %-
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: 45.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-0.62 Å2
2---0.06 Å20 Å2
3---0.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: LAST / Resolution: 1.8→17.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 26 211 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222182
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.9842949
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28925.149101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2815401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3121510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.21004
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.36641376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.52162140
X-RAY DIFFRACTIONr_scbond_it10.1578926
X-RAY DIFFRACTIONr_scangle_it11.95610809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 193 -
Rwork0.285 1668 -
obs--87.87 %
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)
12.8356-0.17820.59521.3540.24221.487-0.04270.30740.1044-0.2460.00810.0119-0.106-0.02320.0346-0.1109-0.03280.0337-0.14240.0133-0.134718.811218.865421.5632
23.94481.83851.32575.1961.3513.79810.1149-0.3330.00670.5342-0.149-0.05490.0077-0.11890.034-0.10920.01850.0108-0.09640.0067-0.165542.135521.854546.8434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 180
2X-RAY DIFFRACTION2A192 - 272

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