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Yorodumi- PDB-2bf2: Crystal structure of native toluene-4-monooxygenase catalytic eff... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bf2 | ||||||
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Title | Crystal structure of native toluene-4-monooxygenase catalytic effector protein, T4moD | ||||||
Components | TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D | ||||||
Keywords | OXIDOREDUCTASE / CATALYTIC EFFECTOR PROTEIN / MAD PHASING / AROMATIC HYDROCARBON CATABOLISM / MONOOXYGENASE / TOLUENE OXIDATION / FAD / FLAVOPROTEIN / IRON | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS MENDOCINA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Lountos, G.T. / Mitchell, K.H. / Studts, J.M. / Fox, B.G. / Orville, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal Structures and Functional Studies of T4Mod, the Toluene 4-Monooxygenase Catalytic Effector Protein Authors: Lountos, G.T. / Mitchell, K.H. / Studts, J.M. / Fox, B.G. / Orville, A.M. #1: Journal: Biochemistry / Year: 2001 Title: Solution Structure of the Toluene-4-Monooxygenase Effector Protein (T4Mod) Authors: Hemmi, H. / Studts, J.M. / Chae, Y.K. / Song, J. / Markley, J.L. / Fox, B.G. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and Preliminary Analysis of Native and N-Terminal Truncated Isoforms of Toluene-4-Monooxygenase Catalytic Effector Protein Authors: Orville, A.M. / Studts, J.M. / Lountos, G.T. / Mitchell, K.H. / Fox, B.G. #3: Journal: Protein Expr.Purif / Year: 1999 Title: Application of Fed-Batch Fermentation to the Preparation of Isotopically Labeled or Selenomethionyl-Labeled Proteins Authors: Studts, J.M. / Fox, B.G. #4: Journal: Biochemistry / Year: 2002 Title: Combined Participation of Hydroxylase Active Site Residues and Effector Protein Binding in a Para to Ortho Modulation of Toluene-4-Monooxygenase Regiospecificity Authors: Mitchell, K.H. / Studts, J.M. / Fox, B.G. #5: Journal: Biochemistry / Year: 1996 Title: Recombinant Toluene-4-Monooxygenase: Catalytic and Mossbauer Studies of the Purified Diiron and Rieske Components of a Four-Protein Complex Authors: Pikus, J.D. / Studts, J.M. / Achim, C. / Kauffmann, K.E. / Munck, E. / Steffan, R.J. / Mcclay, K. / 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 | 2bf2.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bf2.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 2bf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bf2_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 2bf2_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 2bf2_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 2bf2_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/2bf2 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/2bf2 | HTTPS FTP |
-Related 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
#1: Protein | Mass: 11497.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS MENDOCINA (bacteria) / Strain: KR1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q00459, 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: 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: 3.5 Å3/Da / Density % sol: 65 % |
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Crystal grow | pH: 4.7 Details: PROTEIN CRYSTALLIZED FROM 975MM SODIUM/POTASSIUM PHOSPHATE PH 4.7, 400 MM NACL AND 50 MM SUCCINATE PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.7433 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7433 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→37 Å / Num. obs: 19009 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / % possible all: 78.2 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.1→37 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.095 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37 Å
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Refine LS restraints |
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