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- PDB-4kdc: Crystal Structure of UBIG -

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Basic information

Entry
Database: PDB / ID: 4kdc
TitleCrystal Structure of UBIG
Components3-demethylubiquinone-9 3-methyltransferase
KeywordsTRANSFERASE / Rossmann Fold / O-methylation / ubiquinone biosynthesis
Function / homology
Function and homology information


2-polyprenyl-6-hydroxyphenol methylase / 3-demethylubiquinol 3-O-methyltransferase / polyprenyldihydroxybenzoate methyltransferase activity / 3-demethylubiquinol 3-O-methyltransferase activity / 2-polyprenyl-6-hydroxyphenol methylase activity / 2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activity / ubiquinone biosynthesis complex / phosphatidylglycerol binding / hyperosmotic salinity response / ubiquinone biosynthetic process ...2-polyprenyl-6-hydroxyphenol methylase / 3-demethylubiquinol 3-O-methyltransferase / polyprenyldihydroxybenzoate methyltransferase activity / 3-demethylubiquinol 3-O-methyltransferase activity / 2-polyprenyl-6-hydroxyphenol methylase activity / 2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activity / ubiquinone biosynthesis complex / phosphatidylglycerol binding / hyperosmotic salinity response / ubiquinone biosynthetic process / methyltransferase activity / cytoplasmic side of plasma membrane / methylation / cytosol
Similarity search - Function
Ubiquinone biosynthesis O-methyltransferase / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquinone biosynthesis O-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsZhu, Y. / Teng, M. / Li, X.
CitationJournal: Biochem. J. / Year: 2015
Title: Structural and biochemical studies reveal UbiG/Coq3 as a class of novel membrane-binding proteins.
Authors: Zhu, Y. / Wu, B. / Zhang, X. / Fan, X. / Niu, L. / Li, X. / Wang, J. / Teng, M.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-demethylubiquinone-9 3-methyltransferase


Theoretical massNumber of molelcules
Total (without water)27,4201
Polymers27,4201
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.848, 58.584, 40.168
Angle α, β, γ (deg.)90.00, 105.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-demethylubiquinone-9 3-methyltransferase / 2-polyprenyl-6-hydroxyphenyl methylase / 3 / 4-dihydroxy-5-hexaprenylbenzoate methyltransferase / ...2-polyprenyl-6-hydroxyphenyl methylase / 3 / 4-dihydroxy-5-hexaprenylbenzoate methyltransferase / DHHB methyltransferase


Mass: 27420.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ubiG, pufX, yfaB, b2232, JW2226 / Production host: Escherichia coli (E. coli)
References: UniProt: P17993, 3-demethylubiquinol 3-O-methyltransferase, 2-polyprenyl-6-hydroxyphenol methylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5 and 20% polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9994 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 12, 2010
RadiationMonochromator: NiFILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9994 Å / Relative weight: 1
ReflectionResolution: 2.09→29.51 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→29.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22459 777 5 %RANDOM
Rwork0.18271 ---
obs0.18482 14774 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.188 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å2-0 Å2-0.98 Å2
2---0.03 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 75 1718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191680
X-RAY DIFFRACTIONr_bond_other_d00.021593
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9522282
X-RAY DIFFRACTIONr_angle_other_deg3.64833654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14424.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97615266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.726158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211916
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02380
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5312.703866
X-RAY DIFFRACTIONr_mcbond_other1.5312.703865
X-RAY DIFFRACTIONr_mcangle_it2.4344.0391079
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0982.962814
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.146 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 46 -
Rwork0.212 897 -
obs--82.14 %

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