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Yorodumi- PDB-6l2u: Soluble methane monooxygenase reductase FAD-binding domain from M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l2u | ||||||
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Title | Soluble methane monooxygenase reductase FAD-binding domain from Methylosinus sporium. | ||||||
Components | Methane monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Metal-binding / redoxreaction | ||||||
Function / homology | Function and homology information monooxygenase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Methylosinus sporium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Park, J.H. / Ha, S.C. / Rao, Z. / Yoo, H. / Yoon, C. / Kim, S.Y. / Kim, D.S. / Lee, S.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Dalton Trans / Year: 2021 Title: Elucidation of the electron transfer environment in the MMOR FAD-binding domain from Methylosinus sporium 5. Authors: Lee, C. / Ha, S.C. / Rao, Z. / Hwang, Y. / Kim, D.S. / Kim, S.Y. / Yoo, H. / Yoon, C. / Na, J.G. / Park, J.H. / Lee, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l2u.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l2u.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 6l2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/6l2u ftp://data.pdbj.org/pub/pdb/validation_reports/l2/6l2u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 104 - 206 / Label seq-ID: 1 - 103
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-Components
#1: Protein | Mass: 11232.656 Da / Num. of mol.: 2 / Fragment: FAD-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylosinus sporium (bacteria) / Gene: mmoC, C5689_05345 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q27RN2 #2: Chemical | #3: 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: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 10% PEG 3000, 0.1M Na-phosphate dibasic/citric acid pH 4.2, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 32235 / % possible obs: 99.8 % / Redundancy: 14 % / CC1/2: 0.996 / Net I/σ(I): 61.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 1563 / CC1/2: 0.988 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.129 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 58.04 Å2 / Biso mean: 17.046 Å2 / Biso min: 4.73 Å2
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Refinement step | Cycle: final / Resolution: 1.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 112 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.5→1.539 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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