+Open data
-Basic information
Entry | Database: PDB / ID: 4pkc | ||||||
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Title | Benzylsuccinate alpha-gamma complex | ||||||
Components |
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Keywords | LYASE / complex / radical / disorder | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thauera aromatica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Funk, M.A. / Drennan, C.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity. Authors: Funk, M.A. / Judd, E.T. / Marsh, E.N. / Elliott, S.J. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pkc.cif.gz | 194 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pkc.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pkc_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 4pkc_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 4pkc_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 4pkc_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/4pkc ftp://data.pdbj.org/pub/pdb/validation_reports/pk/4pkc | HTTPS FTP |
-Related structure data
Related structure data | 4pkfSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 99117.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68395, benzylsuccinate synthase |
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#2: Protein | Mass: 6865.687 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68394, benzylsuccinate synthase |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.8 % / Description: Large yellow cabouchon with rounded edges |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 1:1 protein (~10 mg/mL in 20 mM HEPES, pH 7.5, 100 mM sodium chloride) to well solution (20-25% PEG400, 50 mM Tris, pH 8.0, 50 mM Bis-Tris, pH 6.5), diffraction-quality crystals typically ...Details: 1:1 protein (~10 mg/mL in 20 mM HEPES, pH 7.5, 100 mM sodium chloride) to well solution (20-25% PEG400, 50 mM Tris, pH 8.0, 50 mM Bis-Tris, pH 6.5), diffraction-quality crystals typically grew within 1 week, cryoprotectant: brief soak in 30% PEG400 + the same buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 30845 / Num. obs: 30845 / % possible obs: 98.3 % / Redundancy: 7 % / Rsym value: 0.148 / Net I/av σ(I): 12.7 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.052 / % possible all: 86.6 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1678) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4PKF Resolution: 2.6→48.972 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.972 Å
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Refine LS restraints |
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LS refinement shell |
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