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Yorodumi- PDB-3dl9: Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dl9 | |||||||||
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Title | Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2 | |||||||||
Components | Cytochrome P450 2R1 | |||||||||
Keywords | OXIDOREDUCTASE / cytochrome p450 / vitamin d / vitamin s 25-hydroxylase / drug metabolism / Structural Genomics / Structural Genomics Consortium / SGC / Disease mutation / Endoplasmic reticulum / Heme / Iron / Membrane / Metal-binding / Microsome / Monooxygenase | |||||||||
Function / homology | Function and homology information vitamin D 25-hydroxylase / vitamin metabolic process / response to cesium ion / calcitriol biosynthetic process from calciol / D3 vitamins binding / Vitamins / Defective CYP27B1 causes VDDR1B / organic acid metabolic process / vitamin D3 25-hydroxylase activity / Vitamin D (calciferol) metabolism ...vitamin D 25-hydroxylase / vitamin metabolic process / response to cesium ion / calcitriol biosynthetic process from calciol / D3 vitamins binding / Vitamins / Defective CYP27B1 causes VDDR1B / organic acid metabolic process / vitamin D3 25-hydroxylase activity / Vitamin D (calciferol) metabolism / vitamin D metabolic process / 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 / response to ionizing radiation / steroid hydroxylase activity / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.721 Å | |||||||||
Authors | Strushkevich, N.V. / Tempel, W. / Gilep, A.A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2. Authors: Strushkevich, N.V. / Tempel, W. / Gilep, A.A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dl9.cif.gz | 208.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dl9.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dl9_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 3dl9_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 3dl9_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 3dl9_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/3dl9 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/3dl9 | HTTPS FTP |
-Related structure data
Related structure data | 3czhS S: Starting model for refinement |
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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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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 55141.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2R1 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q6VVX0, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: Q6VVX0, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor #2: Polysaccharide | #3: Chemical | #4: Chemical | #5: 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: 3.87 Å3/Da / Density % sol: 68.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 1.2M Ammounium sulfate, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.72→50 Å / Num. obs: 46055 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.163 / Χ2: 1.99 / Net I/σ(I): 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3CZH Resolution: 2.721→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.161 / SU B: 10.35 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Programs coot, prodrg, molprobity have also been used in refinement. 3. THE 2-HYDROXYPROPYL-BETA-CYCLODEXTRIN WAS ADDED TO THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Programs coot, prodrg, molprobity have also been used in refinement. 3. THE 2-HYDROXYPROPYL-BETA-CYCLODEXTRIN WAS ADDED TO THE PROTEIN SAMPLE. DUE TO LIMITED RESOLUTION OF THE ELECTRON DENSITY MAP AND LACK OF A PRECISE CHEMICAL DESCRIPTION OF THE ADDITIVE, IT WAS MODELED HERE AS BETA-CYCLODEXTRIN.
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.005 Å2
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Refinement step | Cycle: LAST / Resolution: 2.721→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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