+Open data
-Basic information
Entry | Database: PDB / ID: 4dud | ||||||
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Title | cytochrome P450 BM3h-2G9C6 MRI sensor, no ligand | ||||||
Components | cytochrome P450 BM3 variant 2G9C6 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / MRI contrast sensor / directed evolution | ||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Brustad, E.M. / Lelyveld, V.S. / Snow, C.D. / Crook, N. / Martinez, F.M. / Scholl, T.J. / Jasanoff, A. / Arnold, F.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structure-guided directed evolution of highly selective p450-based magnetic resonance imaging sensors for dopamine and serotonin. Authors: Brustad, E.M. / Lelyveld, V.S. / Snow, C.D. / Crook, N. / Jung, S.T. / Martinez, F.M. / Scholl, T.J. / Jasanoff, A. / Arnold, F.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dud.cif.gz | 402.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dud.ent.gz | 330.5 KB | Display | PDB format |
PDBx/mmJSON format | 4dud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/4dud ftp://data.pdbj.org/pub/pdb/validation_reports/du/4dud | HTTPS FTP |
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-Related structure data
Related structure data | 4dtwC 4dtyC 4dtzC 4du2C 4duaC 4dubC 4ducC 4dueC 4dufC 2ij2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53862.285 Da / Num. of mol.: 2 / Fragment: heme domain, residues 1-465 / Mutation: R51C, F87L, T268A, L437Q, T438L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A1, cyp102 / Production host: Escherichia coli (E. coli) / References: UniProt: P14779, unspecific monooxygenase #2: Chemical | #3: 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: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium cacadylate, pH 5.5, 0.14 M Ca(Ac)2, 14 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→29.808 Å / Num. all: 89987 / Num. obs: 89987 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.074 / Net I/σ(I): 9.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IJ2 Resolution: 1.85→29.808 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.872 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.83 Å2 / Biso mean: 21.4745 Å2 / Biso min: 2.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.808 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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