+Open data
-Basic information
Entry | Database: PDB / ID: 4obx | ||||||
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Title | Crystal structure of yeast Coq5 in the apo form | ||||||
Components | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | ||||||
Keywords | TRANSFERASE / Rossmann Fold / methyltransferase | ||||||
Function / homology | Function and homology information 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase / Ubiquinol biosynthesis / 2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity / extrinsic component of mitochondrial inner membrane / ubiquinone biosynthetic process / aerobic respiration / methylation / mitochondrial inner membrane / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dai, Y.N. / Zhou, K. / Cao, D.D. / Jiang, Y.L. / Meng, F. / Chi, C.B. / Ren, Y.M. / Chen, Y.X. / Zhou, C.Z. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4obx.cif.gz | 202.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4obx.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 4obx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4obx_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 4obx_full_validation.pdf.gz | 474.3 KB | Display | |
Data in XML | 4obx_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 4obx_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4obx ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obx | HTTPS FTP |
-Related structure data
Related structure data | 4obwSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97882 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97882 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.04 Å / Num. obs: 61136 / % possible obs: 98.7 % |
Reflection shell | Resolution: 2.2→2.32 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.911 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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