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Yorodumi- PDB-3gf7: Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gf7 | ||||||
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Title | Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum apoprotein | ||||||
Components | Glutaconyl-CoA decarboxylase subunit A | ||||||
Keywords | LYASE / glutaconyl-CoA decarboxylase / sodium ion transport / biotin / glutamate fermentation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium symbiosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Kress, D. / Brugel, D. / Buckel, W. / Essen, L.-O. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases Authors: Kress, D. / Brugel, D. / Schall, I. / Linder, D. / Buckel, W. / Essen, L.-O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gf7.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gf7.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/3gf7 ftp://data.pdbj.org/pub/pdb/validation_reports/gf/3gf7 | HTTPS FTP |
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-Related structure data
Related structure data | 3gf3C 3glmC 3gmaC 1pixS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65023.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium symbiosum (bacteria) / Strain: HB25 / Gene: gcdA / Plasmid: pASK-IBA7plus / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS / References: UniProt: B7TVP1, glutaconyl-CoA decarboxylase |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.36 Å3/Da / Density % sol: 47.85 % |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8015 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→32.987 Å / Num. obs: 24154 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 9.07 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PIX Resolution: 2.4→32.48 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.86 / SU B: 6.585 / SU ML: 0.159 / SU R Cruickshank DPI: 0.403 / SU Rfree: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.24 Å2 / Biso mean: 31.586 Å2 / Biso min: 9.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→32.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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