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Yorodumi- PDB-6wta: Structure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wta | ||||||
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Title | Structure of F420-H2 Dependent Oxidoreductase (FDOR-A) MSMEG_2027 in complex with F420 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / F420 / Complex / Cofactor | ||||||
Function / homology | F420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / coenzyme F420 binding / FMN-binding split barrel / oxidoreductase activity / plasma membrane / COENZYME F420-4 / Nitroreductase Function and homology information | ||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Jackson, C.J. / Antoney, J.P. | ||||||
Citation | Journal: Biorxiv / Year: 2022 Title: A F420-dependent single domain chemogenetic tool for protein de-dimerization Authors: Antoney, J. / Kainrath, S. / Ahmed, F.H. / Kang, S.W. / Mackie, E.R. / Soares da Costa, T.P. / Jackson, C.J. / Janovjak, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wta.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wta.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wta_validation.pdf.gz | 759.6 KB | Display | wwPDB validaton report |
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Full document | 6wta_full_validation.pdf.gz | 760.8 KB | Display | |
Data in XML | 6wta_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 6wta_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/6wta ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wta | HTTPS FTP |
-Related structure data
Related structure data | 4y9iS 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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-Components
#1: Protein | Mass: 16028.034 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2027 / Plasmid: pETMCSIII / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QU01 #2: Chemical | ChemComp-UBM / | #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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 3.4 Details: 0.07 M citrate, 0.03 M bis-tris propane, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953729987144 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953729987144 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→32.68 Å / Num. obs: 17596 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 19.79 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.078 / Rrim(I) all: 0.183 / Χ2: 0.93 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.556 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 886 / CC1/2: 0.91 / Rpim(I) all: 0.511 / Χ2: 1.02 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y9I Resolution: 1.67→32.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.33 / 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: 1.67→32.68 Å
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Refine LS restraints |
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LS refinement shell |
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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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