+Open data
-Basic information
Entry | Database: PDB / ID: 6kbw | ||||||
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Title | Crystal structure of Tmm from Myroides profundi D25 | ||||||
Components | Trimethylamine monooxygenase | ||||||
Keywords | FLAVOPROTEIN / flavin-containing monooxygenase | ||||||
Function / homology | Function and homology information N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Myroides profundi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.686 Å | ||||||
Authors | Li, C.Y. / Zhang, Y.Z. | ||||||
Citation | Journal: Sci Adv / Year: 2021 Title: Oxidation of trimethylamine to trimethylamine N-oxide facilitates high hydrostatic pressure tolerance in a generalist bacterial lineage. Authors: Qin, Q.L. / Wang, Z.B. / Su, H.N. / Chen, X.L. / Miao, J. / Wang, X.J. / Li, C.Y. / Zhang, X.Y. / Li, P.Y. / Wang, M. / Fang, J. / Lidbury, I. / Zhang, W. / Zhang, X.H. / Yang, G.P. / Chen, Y. / Zhang, Y.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kbw.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kbw.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kbw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6kbw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6kbw_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 6kbw_validation.cif.gz | 63.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/6kbw ftp://data.pdbj.org/pub/pdb/validation_reports/kb/6kbw | HTTPS FTP |
-Related structure data
Related structure data | 5ipyS 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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Unit cell |
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-Components
#1: Protein | Mass: 54932.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myroides profundi (bacteria) / Gene: MPR_3295 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B5RNJ4 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M Magnesium acetate 0.1M Mes, pH 6.5 10%(w/v) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.686→81.96 Å / Num. obs: 115098 / % possible obs: 93.4 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.44 / Num. unique obs: 12333 / Rpim(I) all: 0.317 / % possible all: 69.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IPY Resolution: 1.686→81.956 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.25
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 39.087 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.14 Å2 / Biso mean: 27.91 Å2 / Biso min: 10.69 Å2
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Refinement step | Cycle: final / Resolution: 1.686→81.956 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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