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Yorodumi- PDB-3bpt: Crystal structure of human beta-hydroxyisobutyryl-CoA hydrolase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bpt | ||||||
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Title | Crystal structure of human beta-hydroxyisobutyryl-CoA hydrolase in complex with quercetin | ||||||
Components | 3-hydroxyisobutyryl-CoA hydrolase | ||||||
Keywords | HYDROLASE / COENZYME A / BETA-HYDROXYISOBUTYRYL ACID / QUERCETIN / STRUCTURAL GENOMICS CONSORTIUM / SGC / Branched-chain amino acid catabolism / Disease mutation / Mitochondrion / Transit peptide | ||||||
Function / homology | Function and homology information 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / valine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Pilka, E.S. / Phillips, C. / King, O.N.F. / Guo, K. / von Delft, F. / Pike, A.C.W. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human beta-hydroxyisobutyryl-CoA hydrolase in complex with quercetin. Authors: Pilka, E.S. / Phillips, C. / King, O.N.F. / Guo, K. / von Delft, F. / Pike, A.C.W. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U. | ||||||
History |
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Remark 600 | HETEROGEN PROTEIN WAS CO-CRYSTALLIZED WITH THE PRO-DRUG QUERCETIN, UNDERGOING FAST HYDROLYSIS IN ... HETEROGEN PROTEIN WAS CO-CRYSTALLIZED WITH THE PRO-DRUG QUERCETIN, UNDERGOING FAST HYDROLYSIS IN SOLUTION (P.J. MULHOLLAND ET AL., 2001). THE LIGAND DENSITY WAS MODELLED AS QUERCETIN, AN EXTRA DENSITY PRESENT ABOVE THE C17 HYDROXYL GROUP IS INCONSISTENT WITH THE PRO-DRUG STRUCTURE PUBLISHED AND WAS NOT MODELLED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bpt.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bpt.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bpt ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bpt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41078.516 Da / Num. of mol.: 1 / Fragment: Residues 32-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIBCH / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q6NVY1, 3-hydroxyisobutyryl-CoA hydrolase |
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#2: Chemical | ChemComp-QUE / |
#3: Chemical | ChemComp-HIU / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 293 K / Method: matrix seeding / pH: 5.5 Details: 0.1M Citrate pH 5.5, 20% PEG 3350, 5mM Quercetin added to the protein, MATRIX SEEDING, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97912 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 8, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.05 Å / Num. all: 46971 / Num. obs: 44613 / % possible obs: 83.3 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.073 / Rsym value: 0.044 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2591 / Rsym value: 0.356 / % possible all: 31.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→31 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.741 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.639 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 36.7799 Å / Origin y: -7.8921 Å / Origin z: 14.6141 Å
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