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Yorodumi- PDB-3gnc: Crystal structure of Glutaryl-COA dehydrogenase from Burkholderia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gnc | ||||||
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Title | Crystal structure of Glutaryl-COA dehydrogenase from Burkholderia Pseudomallei with fragment 6421 | ||||||
Components | Glutaryl-CoA dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information glutaryl-CoA dehydrogenase (ETF) / glutaryl-CoA dehydrogenase activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. Authors: Begley, D.W. / Davies, D.R. / Hartley, R.C. / Hewitt, S.N. / Rychel, A.L. / Myler, P.J. / Van Voorhis, W.C. / Staker, B.L. / Stewart, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gnc.cif.gz | 294.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gnc.ent.gz | 239.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnc ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnc | HTTPS FTP |
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-Related structure data
Related structure data | 3d6bSC 3eomC 3eonC 3gqtC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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: 43467.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_3237 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JP94, glutaryl-CoA dehydrogenase #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-QQQ / #4: Chemical | #5: 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: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3000, 0.1M HEPES, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 81993 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.593 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3D6B Resolution: 2.15→46.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.495 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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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: 37.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→46.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 20
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