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Yorodumi- PDB-5tds: Toluene bound in the resting active site of toluene 4-monooxygena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tds | ||||||
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Title | Toluene bound in the resting active site of toluene 4-monooxygenase (T4moH) | ||||||
Components | (Toluene-4-monooxygenase system protein ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / Diiron / hydroxylase / substrate complex | ||||||
Function / homology | Function and homology information toluene 4-monooxygenase / toluene 4-monooxygenase activity / toluene catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas mendocina (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.719 Å | ||||||
Authors | Acheson, J.F. / Fox, B.G. | ||||||
Citation | Journal: Nature / Year: 2017 Title: In-crystal reaction cycle of a toluene-bound diiron hydroxylase. Authors: Acheson, J.F. / Bailey, L.J. / Brunold, T.C. / Fox, B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tds.cif.gz | 769.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tds.ent.gz | 624.6 KB | Display | PDB format |
PDBx/mmJSON format | 5tds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tds_validation.pdf.gz | 482.6 KB | Display | wwPDB validaton report |
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Full document | 5tds_full_validation.pdf.gz | 495.2 KB | Display | |
Data in XML | 5tds_validation.xml.gz | 81.2 KB | Display | |
Data in CIF | 5tds_validation.cif.gz | 122.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/5tds ftp://data.pdbj.org/pub/pdb/validation_reports/td/5tds | HTTPS FTP |
-Related structure data
Related structure data | 5tdtC 5tduC 5tdvC 3dhgS 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
-Toluene-4-monooxygenase system protein ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 57453.438 Da / Num. of mol.: 2 / Fragment: residues 1-493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoA / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP References: UniProt: Q00456, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor #2: Protein | Mass: 38433.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoE / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP References: UniProt: Q00460, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor #3: Protein | Mass: 9600.989 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoB / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP References: UniProt: Q00457, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor |
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-Non-polymers , 5 types, 2016 molecules
#4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-MBN / #7: Chemical | ChemComp-CL / | #8: 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: 1.99 Å3/Da / Density % sol: 38.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM MOPS/HEPES pH 7.5, 100 mM MgCl2, 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98757 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2011 |
Radiation | Monochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98757 Å / Relative weight: 1 |
Reflection | Resolution: 1.719→50 Å / Num. obs: 177282 / % possible obs: 99.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 3.22 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 5.1 % / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3dhg Resolution: 1.719→40.782 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.719→40.782 Å
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Refine LS restraints |
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LS refinement shell |
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