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- PDB-1i4w: THE CRYSTAL STRUCTURE OF THE TRANSCRIPTION FACTOR SC-MTTFB OFFERS... -

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Basic information

Entry
Database: PDB / ID: 1i4w
TitleTHE CRYSTAL STRUCTURE OF THE TRANSCRIPTION FACTOR SC-MTTFB OFFERS INTRIGUING INSIGHTS INTO MITOCHONDRIAL TRANSCRIPTION
ComponentsMITOCHONDRIAL REPLICATION PROTEIN MTF1
KeywordsTRANSCRIPTION / MITOCHONDRIAL TRANSCRIPTION FACTOR / TRANSCRIPTION INITIATION
Function / homology
Function and homology information


Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial transcription / positive regulation of DNA-templated transcription, elongation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / mitochondrial intermembrane space / methylation ...Mitochondrial transcription initiation / mitochondrial DNA-directed RNA polymerase complex / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial transcription / positive regulation of DNA-templated transcription, elongation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / mitochondrial intermembrane space / methylation / mitochondrial matrix / mitochondrion / DNA binding / RNA binding
Similarity search - Function
Mitochondrial transcription factor Mtf1 / rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / 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 ...Mitochondrial transcription factor Mtf1 / rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / 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
XENON / Mitochondrial transcription factor 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6 Å
AuthorsSchubot, F.D. / Chen, C.-J. / Rose, J.P. / Dailey, T.A. / Dailey, H.A. / Wang, B.-C.
CitationJournal: Protein Sci. / Year: 2001
Title: Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription.
Authors: Schubot, F.D. / Chen, C.J. / Rose, J.P. / Dailey, T.A. / Dailey, H.A. / Wang, B.C.
History
DepositionFeb 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL REPLICATION PROTEIN MTF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4884
Polymers41,0941
Non-polymers3943
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.418, 44.684, 99.819
Angle α, β, γ (deg.)90.00, 110.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MITOCHONDRIAL REPLICATION PROTEIN MTF1 / MITOCHONDRIAL TRANSCRIPTION FACTOR MTTFB


Mass: 41094.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MTF1 / Plasmid: PTRCHISC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P14908
#2: Chemical ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, calcium acetate, cacodylate, xylitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Details: Schubot, G.S., (2000) Acta Crystallogr., D56, 902.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2300 mM1reservoirNaCl
310 %glycerol1reservoir
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 21, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 12000 / Num. obs: 10896 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.055 / Net I/σ(I): 19.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.6 / Num. unique all: 852 / Rsym value: 0.2 / % possible all: 63.4
Reflection
*PLUS
Num. measured all: 202625 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 63.4 %

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Processing

Software
NameVersionClassification
ISIRphasing
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.6→19.88 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 382174.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 558 5.2 %RANDOM
Rwork0.187 ---
all0.1914 12000 --
obs0.187 10896 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.07 Å2 / ksol: 0.3669 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å2-2.75 Å2
2--12.56 Å20 Å2
3----13.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 3 21 2673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.511.5
X-RAY DIFFRACTIONc_mcangle_it5.342
X-RAY DIFFRACTIONc_scbond_it5.852
X-RAY DIFFRACTIONc_scangle_it8.192.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 70 5.3 %
Rwork0.255 1245 -
obs--68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88
LS refinement shell
*PLUS
Rfactor Rfree: 0.325 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.255

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