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Yorodumi- PDB-4l6g: Crystal Structure of P450cin Y81F mutant, crystallized in 7 mM 1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l6g | ||||||
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Title | Crystal Structure of P450cin Y81F mutant, crystallized in 7 mM 1,8-cineole | ||||||
Components | P450cin1,8-Cineole 2-endo-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / P450 / heme / monooxygenase / cindoxin | ||||||
Function / homology | Function and homology information 1,8-cineole 2-endo-monooxygenase / carbazole catabolic process / 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 / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Citrobacter braakii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.371 Å | ||||||
Authors | Madrona, Y. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: P450cin active site water: implications for substrate binding and solvent accessibility. Authors: Madrona, Y. / Hollingsworth, S.A. / Khan, B. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l6g.cif.gz | 350.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l6g.ent.gz | 283.7 KB | Display | PDB format |
PDBx/mmJSON format | 4l6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/4l6g ftp://data.pdbj.org/pub/pdb/validation_reports/l6/4l6g | HTTPS FTP |
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-Related structure data
Related structure data | 4l77C 4lhtC 1t2bS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44771.879 Da / Num. of mol.: 2 / Fragment: UNP residues 8-404 / Mutation: Y81F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: CIN A, cinA / Plasmid: pcWori-P450cin / Production host: Escherichia coli (E. coli) / Strain (production host): NEB 5-alpha References: UniProt: Q8VQF6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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-Non-polymers , 5 types, 979 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.2 Details: 15% PEG3350, 100 mM Bis-Tris, pH 6.2, 150 mM lithium sulfate, 7 mM 1,8-cineole, 3 mM TCEP, 100 mM sodium chloride, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 70 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2012 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→34.754 Å / Num. all: 190263 / Num. obs: 185316 / % possible obs: 97.4 % / Observed criterion σ(F): 0.02 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.07 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.37→1.45 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 27034 / Rsym value: 0.472 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T2B Resolution: 1.371→34.754 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.371→34.754 Å
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Refine LS restraints |
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LS refinement shell |
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