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- PDB-3gru: Crystal Structure of the Complex between AMP and Methanocaldococc... -

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Basic information

Entry
Database: PDB / ID: 3gru
TitleCrystal Structure of the Complex between AMP 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 methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / 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 methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / 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 MONOPHOSPHATE / Probable ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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Assembly

Deposited unit
A: Dimethyladenosine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6096
Polymers33,8771
Non-polymers7315
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.528, 66.276, 62.008
Angle α, β, γ (deg.)90.00, 107.52, 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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 333 / 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: 47.53 %
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 18, 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: 1.6→36.85 Å / Num. all: 41383 / Num. obs: 39244 / % possible obs: 94.8 % / Redundancy: 7 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 27.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.15 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4.6 / Num. unique all: 4129 / % possible all: 61.6

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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: 1.6→22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.61 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Residual individual Isotropic B factors wih TLS refinement
Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21211 3921 10 %RANDOM
Rwork0.18094 ---
obs0.18414 35290 94.83 %-
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: 41.155 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.39 Å2
2---0.16 Å20 Å2
3----0.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: LAST / Resolution: 1.6→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 43 333 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222220
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.993020
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17325.5198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.215395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.469158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021648
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21088
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21580
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.82541397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.73962203
X-RAY DIFFRACTIONr_scbond_it7.7278925
X-RAY DIFFRACTIONr_scangle_it9.8110817
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 195 -
Rwork0.258 1577 -
obs--58.42 %
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)
12.1496-0.30020.6221.11160.09251.5397-0.03540.14950.1466-0.1870.0171-0.0345-0.0808-0.02460.0184-0.1424-0.03040.0179-0.1560.0133-0.133918.785618.804121.7721
22.41251.2470.46943.53940.9423.13840.0726-0.16950.07260.4177-0.0751-0.0355-0.0793-0.07580.0025-0.13080.02260.0013-0.12610.0071-0.147442.260821.816946.8638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 180
2X-RAY DIFFRACTION2A192 - 272

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