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- PDB-3grv: Crystal Structure of the Complex between Adenosine and Methanocal... -

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Basic information

Entry
Database: PDB / ID: 3grv
TitleCrystal Structure of the Complex between Adenosine and Methanocaldococcus jannaschi Dim1
ComponentsDimethyladenosine transferase
KeywordsTRANSFERASE / DimethylAdenosine Transferase / Rossmann fold / Ribosomal Assembly S-Adenosyl-L-Methionine / RRNA / 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
ADENOSINE / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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)34,3374
Polymers33,8771
Non-polymers4593
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.263, 66.018, 61.691
Angle α, β, γ (deg.)90.00, 108.35, 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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
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: May 11, 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: 1.9→22.01 Å / Num. all: 24284 / Num. obs: 22955 / % possible obs: 94.5 % / Redundancy: 6.34 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.39 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.5 / % possible all: 96.4

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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: 1.9→22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.576 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Residual Individual Isotropic B factors with TLS refinement
Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23923 1164 5.1 %RANDOM
Rwork0.17967 ---
obs0.18265 21776 94.53 %-
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: 47.732 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.43 Å2
2---0.63 Å20 Å2
3---0.73 Å2
Refine analyzeLuzzati coordinate error obs: 0.252 Å
Refinement stepCycle: LAST / Resolution: 1.9→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 29 218 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222184
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9832959
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62525.347101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.291159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021625
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.21007
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21528
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.17241375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.3362146
X-RAY DIFFRACTIONr_scbond_it10.038926
X-RAY DIFFRACTIONr_scangle_it11.48810813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 71 -
Rwork0.219 1626 -
obs--95.93 %
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)
12.6804-0.40180.98821.4945-0.09391.6250.00520.22570.0747-0.2369-0.0135-0.0099-0.06910.00770.0083-0.1316-0.03160.0305-0.14870.0084-0.168518.513621.087321.5087
24.611.82161.42855.15161.75013.53860.1073-0.28340.12210.4966-0.0913-0.04970.0402-0.0813-0.016-0.12730.02220.0156-0.12270.0103-0.166541.937223.862346.3466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 180
2X-RAY DIFFRACTION2A192 - 269

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