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- PDB-4gc5: Crystal structure of murine TFB1M -

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Basic information

Entry
Database: PDB / ID: 4gc5
TitleCrystal structure of murine TFB1M
ComponentsDimethyladenosine transferase 1, mitochondrial
KeywordsTRANSFERASE / Methyltransferase fold / rRNA Methyltransferase / S-adenosyl-L-methionine (SAM) binding / Methylation / Mitochondria
Function / homology
Function and homology information


rRNA (adenine-N6,N6-)-dimethyltransferase activity / S-adenosyl-L-methionine binding / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / Dimethyladenosine transferase 1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.801 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 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)39,4663
Polymers39,3481
Non-polymers1182
Water4,197233
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)78,9326
Polymers78,6962
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3970 Å2
ΔGint-36 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.630, 101.270, 211.660
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.24 Å3/Da / Density % sol: 62.08 %
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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.801→40 Å / Num. obs: 33212

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 1.801→33.418 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 1678 5.05 %Random
Rwork0.1843 ---
obs0.1863 33212 69.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→33.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 8 233 2746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132616
X-RAY DIFFRACTIONf_angle_d1.5153557
X-RAY DIFFRACTIONf_dihedral_angle_d15.212997
X-RAY DIFFRACTIONf_chiral_restr0.101410
X-RAY DIFFRACTIONf_plane_restr0.007457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.85380.2949370.2838595X-RAY DIFFRACTION16
1.8538-1.91360.3406590.28381104X-RAY DIFFRACTION30
1.9136-1.9820.3458740.27531506X-RAY DIFFRACTION40
1.982-2.06130.29731030.25811824X-RAY DIFFRACTION49
2.0613-2.15510.248990.24742187X-RAY DIFFRACTION58
2.1551-2.26870.31381420.28422543X-RAY DIFFRACTION68
2.2687-2.41080.26921480.23642981X-RAY DIFFRACTION79
2.4108-2.59690.26381800.23843472X-RAY DIFFRACTION92
2.5969-2.85810.26612080.21813794X-RAY DIFFRACTION100
2.8581-3.27140.2421890.19053833X-RAY DIFFRACTION100
3.2714-4.12040.19082300.13593816X-RAY DIFFRACTION100
4.1204-33.4180.16622090.13563879X-RAY DIFFRACTION96
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)
11.323-0.6896-0.24377.4911-1.24051.7888-0.13940.1530.1089-0.2150.5503-0.5756-0.44180.7643-0.45330.6875-0.2178-0.03770.6641-0.11240.41122.2652-9.359197.7419
22.5086-0.1377-0.84311.5097-1.17235.32540.0628-0.43670.07070.2070.08570.1185-0.0259-0.2738-0.14150.3314-0.11410.0310.3437-0.01940.29027.891226.13783.9696
33.8386-0.2808-0.73360.94750.28363.40050.1569-0.2999-0.0163-0.007-0.1055-0.03160.0820.2241-0.03960.2774-0.0704-0.00030.27840.10340.327228.134824.944959.1993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 241 )
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 328 )

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