+Open data
-Basic information
Entry | Database: PDB / ID: 6gpe | ||||||
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Title | Crystal Structure of the CsiD Glutarate Hydroxylase | ||||||
Components | Protein CsiD | ||||||
Keywords | HYDROLASE / jelly roll / glutarate hydroxylase / alpha-ketoglutarate-dependent | ||||||
Function / homology | Function and homology information response to carbon starvation / glutarate dioxygenase activity / glutarate dioxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated / L-lysine catabolic process / ferrous iron binding / iron ion binding / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Williams, R.M. / Mayans, O. / Hartig, J.S. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Authors: Knorr, S. / Sinn, M. / Galetskiy, D. / Williams, R.M. / Wang, C. / Muller, N. / Mayans, O. / Schleheck, D. / Hartig, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gpe.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gpe.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gpe_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 6gpe_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 6gpe_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 6gpe_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/6gpe ftp://data.pdbj.org/pub/pdb/validation_reports/gp/6gpe | HTTPS FTP |
-Related structure data
Related structure data | 6gpnC 6hl8C 6hl9C 2r6sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40646.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: csiD, gab, ygaT, b2659, JW5427 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76621 #2: Chemical | #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: 3.09 Å3/Da / Density % sol: 60.25 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.08 M Sodium chloride, 0.012 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→45.67 Å / Num. obs: 158775 / % possible obs: 96.58 % / Redundancy: 23.3 % / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.53→1.57 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2r6s Resolution: 2.2→42.505 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→42.505 Å
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Refine LS restraints |
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LS refinement shell |
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