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Yorodumi- PDB-7snm: Lanosterol-bound P450 domain of the CYP51-ferredoxin fusion prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7snm | ||||||
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Title | Lanosterol-bound P450 domain of the CYP51-ferredoxin fusion protein from Methylococcus capsulatus | ||||||
Components | Cytochrome P450 51 | ||||||
Keywords | OXIDOREDUCTASE / CYTOCHROME P450 FOLD / CYP51 / HEME / STEROL BIOSYNTHESIS | ||||||
Function / homology | Function and homology information sterol 14alpha-demethylase / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Methylococcus capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Lepesheva, G.I. / Hargrove, T. / Wawrzak, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Unravelling the role of transient redox partner complexes in P450 electron transfer mechanics. Authors: Hargrove, T.Y. / Lamb, D.C. / Smith, J.A. / Wawrzak, Z. / Kelly, S.L. / Lepesheva, G.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7snm.cif.gz | 755.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7snm.ent.gz | 624.8 KB | Display | PDB format |
PDBx/mmJSON format | 7snm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7snm_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 7snm_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7snm_validation.xml.gz | 68.9 KB | Display | |
Data in CIF | 7snm_validation.cif.gz | 91.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/7snm ftp://data.pdbj.org/pub/pdb/validation_reports/sn/7snm | HTTPS FTP |
-Related structure data
Related structure data | 6mi0S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 6 - 448 / Label seq-ID: 6 - 448
NCS ensembles :
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-Components
#1: Protein | Mass: 62483.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria) Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: cyp51, MCA2711 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS-164 / References: UniProt: Q603T8, sterol 14alpha-demethylase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-LAN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.1 Details: Na-citrate tribasic dehydrate, PEG 8,000, dodecyltrimethylammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 10, 2021 / Details: Focussing mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→74.45 Å / Num. obs: 67008 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.55→2.62 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4997 / CC1/2: 0.96 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6mi0 Resolution: 2.55→74.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.883 / SU B: 30.255 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 289.91 Å2 / Biso mean: 54.83 Å2 / Biso min: 11.91 Å2
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Refinement step | Cycle: final / Resolution: 2.55→74.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / 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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