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Yorodumi- PDB-4umz: PikC D50N mutant in complex with the engineered substrate mimic b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4umz | ||||||
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Title | PikC D50N mutant in complex with the engineered substrate mimic bearing a 2-dimethylaminomethylbenzoate group | ||||||
Components | CYTOCHROME P450 HYDROXYLASE PIKC | ||||||
Keywords | ELECTRON TRANSPORT / 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: 2.32 Å | ||||||
Authors | Podust, L.M. / Vieira, D.F. | ||||||
Citation | Journal: To be Published Title: Recognition of Synthetic Substrates by P450 Pikc Authors: Podust, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4umz.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4umz.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 4umz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4umz_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 4umz_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4umz_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 4umz_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/4umz ftp://data.pdbj.org/pub/pdb/validation_reports/um/4umz | HTTPS FTP |
-Related structure data
Related structure data | 3zpiC 4b7dC 4bf4C 2vzmS 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 Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: O87605 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.69 Å3/Da / Density % sol: 54.4 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 4% TACSIMATE, PH 5.5, 16% PEG3350, 0.1M NA CITRATE, PH 5.6 |
-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: Mar 26, 2014 / 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: 2.32→151.62 Å / Num. obs: 40952 / % possible obs: 93.5 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.32→2.45 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / % possible all: 69.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VZM Resolution: 2.32→62.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.202 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.246 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.859 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→62.63 Å
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Refine LS restraints |
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