+Open data
-Basic information
Entry | Database: PDB / ID: 8k41 | ||||||
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Title | mercuric reductase,GbsMerA, - FAD bound | ||||||
Components | NAD(P)/FAD-dependent oxidoreductase | ||||||
Keywords | TRANSFERASE / Mercuric reductase / Gelidibacter salicanalis PAMC21136 / Hg resistance / Heavy metal detoxification | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gelidibacter salicanalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Do, H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Sci Rep / Year: 2023 Title: Biochemical and structural basis of mercuric reductase, GbsMerA, from Gelidibacter salicanalis PAMC21136. Authors: Pardhe, B.D. / Lee, M.J. / Lee, J.H. / Do, H. / Oh, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k41.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k41.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 8k41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/8k41 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/8k41 | HTTPS FTP |
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-Related structure data
Related structure data | 8k40C C: citing same article (ref.) |
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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: 49953.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gelidibacter salicanalis (bacteria) / Gene: JEM65_00875 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A934NG65 |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
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: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.12M of ethylene glycol, 0.1M bicine/Trizma pH8.5 |
-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: 0.9794 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→29.57 Å / Num. obs: 26169 / % possible obs: 99 % / Redundancy: 20.1 % / CC1/2: 1 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 2.39→2.48 Å / Num. unique obs: 2695 / CC1/2: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→29.57 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.268 / SU ML: 0.211 / Cross valid method: FREE R-VALUE / ESU R: 0.296 / ESU R Free: 0.25 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→29.57 Å
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Refine LS restraints |
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LS refinement shell |
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