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Yorodumi- PDB-3zk5: PikC D50N mutant bound to the 10-DML analog with the 3-(N,N-dimet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zk5 | ||||||
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Title | PikC D50N mutant bound to the 10-DML analog with the 3-(N,N-dimethylamino)ethanoate anchoring group | ||||||
Components | CYTOCHROME P450 HYDROXYLASE PIKC | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / PIKROMYCIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information pikromycin synthase / macrolide biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES VENEZUELAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Podust, L.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Directing Group-Controlled Regioselectivity in an Enzymatic C-H Bond Oxygenation. Authors: Negretti, S. / Narayan, A.R.H. / Chiou, K.C. / Kells, P.M. / Stachowski, J.L. / Hansen, D.A. / Podust, L.M. / Montgomery, J. / Sherman, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zk5.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zk5.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 3zk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zk5_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3zk5_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3zk5_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 3zk5_validation.cif.gz | 54.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/3zk5 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zk5 | HTTPS FTP |
-Related structure data
Related structure data | 4b7sSC 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
#1: Protein | Mass: 48267.758 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THIOLATE LINK BETWEEN C 354 AND HEM 1407 / Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: O87605 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | NA (Z18): SYNTHETIC SUBSTRATE DERIVATIVE | Sequence details | FIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN CLEAVAGE SITE ARE FROM THE CLONING VECTOR ...FIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A D50N MUTATION IS ENGINEERED | |
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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: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.2 MGCL, 20% PEG 3350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 11, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→92.38 Å / Num. obs: 54311 / % possible obs: 89.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.89→1.99 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.5 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B7S Resolution: 1.89→69.25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.88 / SU B: 4.376 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 21.193 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→69.25 Å
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Refine LS restraints |
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