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- PDB-4obx: Crystal structure of yeast Coq5 in the apo form -

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Basic information

Entry
Database: PDB / ID: 4obx
TitleCrystal structure of yeast Coq5 in the apo form
Components2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
KeywordsTRANSFERASE / Rossmann Fold / methyltransferase
Function / homology
Function and homology information


2-methoxy-6-polyprenyl-1,4-benzoquinol methylase / : / : / extrinsic component of mitochondrial inner membrane / ubiquinone biosynthetic process / aerobic respiration / methyltransferase activity / methylation / mitochondrial inner membrane / mitochondrial matrix / mitochondrion
Similarity search - Function
UbiE/COQ5 methyltransferase / ubiE/COQ5 methyltransferase family signature 1. / UbiE family SAM-binding methyltransferase profile. / ubiE/COQ5 methyltransferase family signature 2. / UbiE/COQ5 methyltransferase, conserved site / ubiE/COQ5 methyltransferase family / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDai, Y.N. / Zhou, K. / Cao, D.D. / Jiang, Y.L. / Meng, F. / Chi, C.B. / Ren, Y.M. / Chen, Y.X. / Zhou, C.Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystal structures and catalytic mechanism of the C-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway.
Authors: Dai, Y.N. / Zhou, K. / Cao, D.D. / Jiang, Y.L. / Meng, F. / Chi, C.B. / Ren, Y.M. / Chen, Y. / Zhou, C.Z.
History
DepositionJan 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 20, 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_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

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Assembly

Deposited unit
A: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
D: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
C: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
B: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3356
Polymers117,0094
Non-polymers3262
Water7,837435
1
A: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
B: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6683
Polymers58,5042
Non-polymers1631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-31 kcal/mol
Surface area20850 Å2
MethodPISA
2
D: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
C: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6683
Polymers58,5042
Non-polymers1631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-32 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.270, 75.640, 84.480
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / Ubiquinone biosynthesis methyltransferase COQ5


Mass: 29252.207 Da / Num. of mol.: 4 / Fragment: core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: COQ5, DBI56, YM8339.09C, YML110C / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P49017, 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase
#2: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% (w/v) 2-propanol, 20% (w/v) polyethylene glycol 4000, 0.1 M sodium citrate tribasic, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97882 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97882 Å / Relative weight: 1
ReflectionResolution: 2.2→49.04 Å / Num. obs: 61136 / % possible obs: 98.7 %
Reflection shellResolution: 2.2→2.32 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4OBW

4obw


Resolution: 2.2→49.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.17 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24785 3081 5 %RANDOM
Rwork0.20453 ---
obs0.20672 58051 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0 Å21.22 Å2
2--0.37 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7500 0 22 435 7957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027688
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.95710352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3685936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48724.624372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.216151364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8251536
X-RAY DIFFRACTIONr_chiral_restr0.0750.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215840
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 189 -
Rwork0.373 4229 -
obs--99.01 %

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