+Open data
-Basic information
Entry | Database: PDB / ID: 2inn | ||||||
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Title | Structure of the Phenol Hydroxyalse-Regulatory Protein Complex | ||||||
Components | (Phenol hydroxylase component ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE / hydroxylase / four-helix bundle / diiron / phenol / complex | ||||||
Function / homology | Function and homology information phenol 2-monooxygenase activity / 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 / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Sazinsky, M.H. / Dunten, P.W. / McCormick, M.S. / Lippard, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: X-ray Structure of a Hydroxylase-Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase. Authors: Sazinsky, M.H. / Dunten, P.W. / McCormick, M.S. / Didonato, A. / 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 | 2inn.cif.gz | 408 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2inn.ent.gz | 346.4 KB | Display | PDB format |
PDBx/mmJSON format | 2inn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/2inn ftp://data.pdbj.org/pub/pdb/validation_reports/in/2inn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is an alpha, beta, gamma heterodimer complexed to one molecule of the regulatory protein. The molecule in asymmetric unit is the biologically relavent asembly. |
-Components
-Phenol hydroxylase component ... , 4 types, 7 molecules ABCDEFL
#1: Protein | Mass: 61058.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phN / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ2 #2: Protein | Mass: 39255.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phL / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ4 #3: Protein | Mass: 13482.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phO / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ1 #4: Protein | | Mass: 10770.048 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phM / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ3 |
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-Non-polymers , 4 types, 311 molecules
#5: Chemical | ChemComp-FE / #6: Chemical | #7: Chemical | ChemComp-MOO / | #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: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Tris, pH 7.0, 150 mM Na2MoO4, 5% glycerol, and 17-20% PEG 8000 (w/w), VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 68087 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / Num. unique all: 2565 / Rsym value: 0.26 / % possible all: 54 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.992 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.988 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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