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Yorodumi- PDB-3gf3: Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gf3 | ||||||
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Title | Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with glutaconyl-coA | ||||||
Components | Glutaconyl-CoA decarboxylase subunit A | ||||||
Keywords | LYASE / glutaconyl-CoA decarboxylase / sodium ion transport / biotin / glutamate fermentation | ||||||
Function / homology | Function and homology information methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / L-leucine catabolic process / lyase activity Similarity search - Function | ||||||
Biological species | Clostridium symbiosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 | 3gf3.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gf3.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gf3_validation.pdf.gz | 685.1 KB | Display | wwPDB validaton report |
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Full document | 3gf3_full_validation.pdf.gz | 691.7 KB | Display | |
Data in XML | 3gf3_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 3gf3_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/3gf3 ftp://data.pdbj.org/pub/pdb/validation_reports/gf/3gf3 | HTTPS FTP |
-Related structure data
Related structure data | 3gf7C 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 on special symmetry positions |
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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, EC: 4.1.1.70 |
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#2: Chemical | ChemComp-COO / |
#3: Chemical | ChemComp-CL / |
#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: 2.37 Å3/Da / Density % sol: 48.19 % |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54179 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→37.349 Å / Num. obs: 60672 / % possible obs: 97.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 10.391 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.75→36.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.17 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.899 / SU B: 1.807 / SU ML: 0.059 / SU R Cruickshank DPI: 0.103 / SU Rfree: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.091 / 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: 68.2 Å2 / Biso mean: 23.183 Å2 / Biso min: 11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→36.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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