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Yorodumi- PDB-4rhp: Crystal structure of human COQ9 in complex with a phospholipid, N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rhp | ||||||
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Title | Crystal structure of human COQ9 in complex with a phospholipid, Northeast Structural Genomics Consortium Target HR5043 | ||||||
Components | Ubiquinone biosynthesis protein COQ9, mitochondrialCoenzyme Q10 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / all alpha-helical protein / Ubiquinone biosynthesis / mitochondrial / Mitochondrial Protein Partnership / MPP | ||||||
Function / homology | Function and homology information Ubiquinol biosynthesis / ubiquinone biosynthesis complex / ubiquinone biosynthetic process / mitochondrial electron transport, NADH to ubiquinone / mitochondrial inner membrane / lipid binding / protein homodimerization activity / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.393 Å | ||||||
Authors | Forouhar, F. / Lew, S. / Seetharaman, J. / Wang, H. / Lee, D. / Kogan, S. / Maglaqui, M. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Wang, H. / Lee, D. / Kogan, S. / Maglaqui, M. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Authors: Lohman, D.C. / Forouhar, F. / Beebe, E.T. / Stefely, M.S. / Minogue, C.E. / Ulbrich, A. / Stefely, J.A. / Sukumar, S. / Luna-Sanchez, M. / Jochem, A. / Lew, S. / Seetharaman, J. / Xiao, R. / ...Authors: Lohman, D.C. / Forouhar, F. / Beebe, E.T. / Stefely, M.S. / Minogue, C.E. / Ulbrich, A. / Stefely, J.A. / Sukumar, S. / Luna-Sanchez, M. / Jochem, A. / Lew, S. / Seetharaman, J. / Xiao, R. / Wang, H. / Westphall, M.S. / Wrobel, R.L. / Everett, J.K. / Mitchell, J.C. / Lopez, L.C. / Coon, J.J. / Tong, L. / Pagliarini, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rhp.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rhp.ent.gz | 142.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/4rhp ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rhp | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27091.748 Da / Num. of mol.: 2 / Fragment: residues 84-318 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75208 #2: Chemical | ChemComp-PEF / | #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: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | Temperature: 291 K / Method: mircobatch under oil / pH: 8.5 Details: 100 mM TRIS (pH 8.5), 20% (v/v) PEG 3350, and 200 mM MgCl2 , mircobatch under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 7, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.79 Å / Num. obs: 35868 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.061 / Net I/σ(I): 15.68 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.55 / Num. unique all: 3589 / Rsym value: 0.464 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.393→48.79 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.647 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.393→48.79 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -13.6155 Å / Origin y: -24.8997 Å / Origin z: -33.7711 Å
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Refinement TLS group | Selection details: all |