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Yorodumi- PDB-6laa: Crystal structure of full-length CYP116B46 from Tepidiphilus ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6laa | ||||||
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Title | Crystal structure of full-length CYP116B46 from Tepidiphilus thermophilus | ||||||
Components | Cytochrome P450 | ||||||
Keywords | HYDROLASE / ANTIBIOTICS / BIOSYNTHESIS | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding / nucleotide binding / heme binding Similarity search - Function | ||||||
Biological species | Tepidiphilus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Zhang, L.L. / Ko, T.P. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase. Authors: Zhang, L.L. / Xie, Z.Z. / Liu, Z.W. / Zhou, S.Y. / Ma, L.X. / Liu, W.D. / Huang, J.W. / Ko, T.P. / Li, X.Q. / Hu, Y.C. / Min, J. / Yu, X.J. / Guo, R.T. / Chen, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6laa.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6laa.ent.gz | 143.8 KB | Display | PDB format |
PDBx/mmJSON format | 6laa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6laa_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 6laa_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 6laa_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 6laa_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6laa ftp://data.pdbj.org/pub/pdb/validation_reports/la/6laa | HTTPS FTP |
-Related structure data
Related structure data | 6ldlC 6giiS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 89544.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tepidiphilus thermophilus (bacteria) / Plasmid: pRSF-Duet I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K6ITW2 |
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-Non-polymers , 7 types, 561 molecules
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-FES / | ||
#4: Chemical | ChemComp-FMN / | ||
#5: Chemical | ChemComp-IMD / | ||
#6: Chemical | ChemComp-CO3 / | ||
#7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
-Details
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: 3.04 Å3/Da / Density % sol: 59.52 % / Mosaicity: 0.487 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: Na/K phosphate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2 cooled Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.13→25 Å / Num. obs: 62367 / % possible obs: 99.7 % / Redundancy: 16.5 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.028 / Rrim(I) all: 0.113 / Χ2: 0.89 / Net I/σ(I): 6 / Num. measured all: 1025951 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GII Resolution: 2.13→24.11 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.17 Å2 / Biso mean: 46.2346 Å2 / Biso min: 23.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.13→24.11 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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