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Yorodumi- PDB-8w72: Crystal structure of a P450 enzyme DmlH that catalyze intramolecu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w72 | ||||||||||||
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Title | Crystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins | ||||||||||||
Components | Cytochrome P450 | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / P450 enzyme / intramolecular phenol coupling / cihanmycins | ||||||||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE Function and homology information | ||||||||||||
Biological species | Streptomyces sp. DM14 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||||||||
Authors | Fang, C. / Zhang, L. / Zhu, Y. / Zhang, C. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Crystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins Authors: Fang, C. / Zhang, L. / Zhu, Y. / Zhang, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w72.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w72.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 8w72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/8w72 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/8w72 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46858.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. DM14 (bacteria) |
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#2: Chemical | ChemComp-HEM / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.3 M CaCl2, 0.3 M MgCl2, 0.5 M MES, 0.5 M imidazole, 37.5% w/v PEG 1K_PEG 3350_MPD, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→53.49 Å / Num. obs: 6132 / % possible obs: 92.4 % / Redundancy: 7.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.058 / Rrim(I) all: 0.162 / Χ2: 0.93 / Net I/σ(I): 9.5 / Num. measured all: 45745 |
Reflection shell | Resolution: 3.25→3.43 Å / % possible obs: 91.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.541 / Num. measured all: 3695 / Num. unique obs: 844 / CC1/2: 0.805 / Rpim(I) all: 0.26 / Rrim(I) all: 0.605 / Χ2: 0.75 / Net I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→50.22 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.32 / 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 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→50.22 Å
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Refine LS restraints |
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LS refinement shell |
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