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- PDB-4gc9: Crystal structure of murine TFB1M in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 4gc9
TitleCrystal structure of murine TFB1M in complex with SAM
ComponentsDimethyladenosine transferase 1, mitochondrial
KeywordsTRANSFERASE / Methyltransferase fold / rRNA methyltransferase / S-adenosyl-L-methionine / Methylation / Mitochondria
Function / homology
Function and homology information


mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / mitochondrial matrix / mitochondrion / DNA binding / RNA binding
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
ACETATE ION / S-ADENOSYLMETHIONINE / Dimethyladenosine transferase 1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsGuja, K.E. / Yakubovskaya, E. / Shi, H. / Mejia, E. / Hambardjieva, E. / Venkataraman, K. / Karzai, A.W. / Garcia-Diaz, M.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1.
Authors: Guja, K.E. / Venkataraman, K. / Yakubovskaya, E. / Shi, H. / Mejia, E. / Hambardjieva, E. / Karzai, A.W. / Garcia-Diaz, M.
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethyladenosine transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8053
Polymers39,3481
Non-polymers4572
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dimethyladenosine transferase 1, mitochondrial
hetero molecules

A: Dimethyladenosine transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6116
Polymers78,6962
Non-polymers9154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area3530 Å2
ΔGint-34 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.700, 101.680, 211.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Dimethyladenosine transferase 1, mitochondrial / Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / mtTFB1 / S- ...Mitochondrial 12S rRNA dimethylase 1 / Mitochondrial transcription factor B1 / mtTFB1 / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase 1


Mass: 39347.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tfb1m / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express RIL (DE3)
References: UniProt: Q8JZM0, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.9 M Sodium Acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.103→40 Å / Num. obs: 23216

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4GC5

4gc5


Resolution: 2.103→33.467 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1189 5.12 %Random
Rwork0.2052 ---
obs0.2067 23216 76.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→33.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 31 149 2661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032624
X-RAY DIFFRACTIONf_angle_d0.6833577
X-RAY DIFFRACTIONf_dihedral_angle_d12.77998
X-RAY DIFFRACTIONf_chiral_restr0.047415
X-RAY DIFFRACTIONf_plane_restr0.003456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.103-2.19850.1794370.1965870X-RAY DIFFRACTION24
2.1985-2.31440.2634920.23261650X-RAY DIFFRACTION46
2.3144-2.45930.29491210.25312328X-RAY DIFFRACTION65
2.4593-2.64920.27831780.26162963X-RAY DIFFRACTION83
2.6492-2.91560.28632020.25753529X-RAY DIFFRACTION99
2.9156-3.33720.24622080.233579X-RAY DIFFRACTION99
3.3372-4.20320.18671920.16743618X-RAY DIFFRACTION99
4.2032-33.4670.21711590.17583490X-RAY DIFFRACTION90
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)
10.5721-0.32030.18780.35310.06930.18780.120.36390.0705-0.05710.4054-0.1703-0.040.4626-0.00740.5792-0.2550.06870.4067-0.1410.4795-21.3517-59.6021-8.9854
21.16480.25490.06421.0482-0.16672.4741-0.0094-0.2182-0.01320.24190.12220.15320.151-0.2282-0.03780.1997-0.13550.02910.20970.00510.1166-15.997-24.4571-21.9196
31.7154-0.2202-0.24660.81150.09791.57640.8248-0.0431-0.1431-0.7781-0.66140.14120.96530.9442-0.0166-0.3176-0.53450.2557-0.42720.3127-0.01314.3259-25.599-46.5852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 241 )
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 327 )

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