+Open data
-Basic information
Entry | Database: PDB / ID: 2cd8 | ||||||
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Title | Crystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1) | ||||||
Components | CYTOCHROME P450 MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / CYTOCHROME P450 / PIKC / YC-17 / MACROLIDE MONOOXYGENASE / ANTIBIOTIC BIOSYNTHESIS / HEME / IRON / METAL-BINDING | ||||||
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: 1.7 Å | ||||||
Authors | Yermalitskaya, L.I. / Kim, Y. / Sherman, D.H. / Waterman, M.R. / Podust, L.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The Structural Basis for Substrate Anchoring, Active Site Selectivity, and Product Formation by P450 Pikc from Streptomyces Venezuelae. Authors: Sherman, D.H. / Li, S. / Yermalitskaya, L.V. / Kim, Y. / Smith, J.A. / Waterman, M.R. / 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 | 2cd8.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cd8.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cd8_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2cd8_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2cd8_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 2cd8_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cd8 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cd8 | HTTPS FTP |
-Related structure data
Related structure data | 2bvjSC 2c6hC 2c7xC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99785, 0.04482, 0.04776), Vector: |
-Components
#1: Protein | Mass: 48268.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / 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 PET28A | |
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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: 1.93 Å3/Da / Density % sol: 35 % |
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Crystal grow | pH: 7.5 Details: 20% PEG 3350, 0.2 M MGCL2, 0.5 MM DTT, 1 MM YC-17, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97872 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 20, 2005 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 78149 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BVJ Resolution: 1.7→39.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 153672.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.4233 Å2 / ksol: 0.372924 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→39.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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