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Yorodumi- PDB-5bwe: Benzylsuccinate synthase alpha-beta-gamma complex with bound tolu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bwe | |||||||||
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Title | Benzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate | |||||||||
Components | (benzylsuccinate synthase ...) x 3 | |||||||||
Keywords | LYASE / radical / complex | |||||||||
Function / homology | Function and homology information 4 iron, 4 sulfur cluster binding / lyase activity / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Thauera aromatica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Funk, M.A. / Drennan, C.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation. Authors: Funk, M.A. / Marsh, E.N. / 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 | 5bwe.cif.gz | 390.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bwe.ent.gz | 313.8 KB | Display | PDB format |
PDBx/mmJSON format | 5bwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bwe_validation.pdf.gz | 523.6 KB | Display | wwPDB validaton report |
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Full document | 5bwe_full_validation.pdf.gz | 535.4 KB | Display | |
Data in XML | 5bwe_validation.xml.gz | 62.6 KB | Display | |
Data in CIF | 5bwe_validation.cif.gz | 83.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/5bwe ftp://data.pdbj.org/pub/pdb/validation_reports/bw/5bwe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Benzylsuccinate synthase ... , 3 types, 6 molecules ADBFCG
#1: Protein | Mass: 99117.109 Da / Num. of mol.: 2 / Mutation: M789I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutD / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68395, benzylsuccinate synthase #2: Protein | Mass: 9303.302 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutG / Plasmid: pRSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68396 #3: Protein | Mass: 6865.687 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thauera aromatica (bacteria) / Strain: T1 / Gene: tutF / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68394 |
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-Non-polymers , 3 types, 6 molecules
#4: Chemical | #5: Chemical | #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2:1 8 mg/mL BSS-alpha-beta-gamma (in 50 mM Tris, pH 7.6, 15% v/v glycerol, 200 mM sodium chloride) to well solution (25% w/v PEG3350, 100 mM Tris, pH 8.5, 60 mM potassium chloride, 5 mM ...Details: 2:1 8 mg/mL BSS-alpha-beta-gamma (in 50 mM Tris, pH 7.6, 15% v/v glycerol, 200 mM sodium chloride) to well solution (25% w/v PEG3350, 100 mM Tris, pH 8.5, 60 mM potassium chloride, 5 mM fumarate), 1-2 uL toluene was added to the bottom of the well and allowed to diffuse slowly into the protein drop, diffraction-quality crystals grew over the course of three weeks in a temperature-controlled anaerobic chamber |
-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 315r / Detector: CCD / Date: Jul 19, 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: 3.3→40 Å / Num. obs: 30311 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rsym value: 0.101 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.3 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→38.27 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→38.27 Å
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Refine LS restraints |
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LS refinement shell |
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