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Yorodumi- PDB-3n20: X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n20 | ||||||
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Title | X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase T201V Mutant | ||||||
Components | (Toluene o-xylene monooxygenase ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / Diiron / 4-helix bundle / carboxylate bridge / metalloenzyme | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / : / monooxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | McCormick, M.S. / Sazinsky, M.H. / Lippard, S.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Active Site Threonine Facilitates Proton Transfer during Dioxygen Activation at the Diiron Center of Toluene/o-Xylene Monooxygenase Hydroxylase. Authors: Song, W.J. / McCormick, M.S. / Behan, R.K. / Sazinsky, M.H. / Jiang, W. / Lin, J. / Krebs, C. / Lippard, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n20.cif.gz | 209.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n20.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 3n20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/3n20 ftp://data.pdbj.org/pub/pdb/validation_reports/n2/3n20 | HTTPS FTP |
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-Related structure data
Related structure data | 3n1xC 3n1yC 3n1zC 2incS 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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2 |
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Unit cell |
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-Components
-Toluene o-xylene monooxygenase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 57784.672 Da / Num. of mol.: 1 / Fragment: alpha subunit / Mutation: T201V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: OX1 / Gene: touA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IV66 |
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#2: Protein | Mass: 38381.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: OX1 / Gene: touE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IV62 |
#3: Protein | Mass: 9986.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: OX1 / Gene: touB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IV65 |
-Non-polymers , 4 types, 570 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-P6G / #6: Chemical | #7: 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: 3.12 Å3/Da / Density % sol: 60.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 2.1-2.5 M Ammonium Sulfate, 2-4% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2008 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 102888 / Num. obs: 98258 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.098 |
Reflection shell | Resolution: 1.9→2.05 Å / Rsym value: 0.66 / % possible all: 84.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2INC Resolution: 1.9→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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