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Yorodumi- PDB-6kod: Cu(II) complex of HOCl-induced flavoprotein disulfide reductase R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kod | ||||||
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Title | Cu(II) complex of HOCl-induced flavoprotein disulfide reductase RclA C43S mutant from Escherichia coli | ||||||
Components | Pyridine nucleotide-disulphide oxidoreductase dimerisation region | ||||||
Keywords | OXIDOREDUCTASE / Flavoprotein / hypochlorous acid / reductase / cysteine disulfide / copper / cupric ion | ||||||
Function / homology | Function and homology information response to hypochlorite / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / cupric reductase (NADH) activity / oxidoreductase activity, acting on NAD(P)H / flavin adenine dinucleotide binding / nucleotide binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Baek, Y. / Ha, N.-C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structure and function of the hypochlorous acid-induced flavoprotein RclA fromEscherichia coli. Authors: Baek, Y. / Kim, J. / Ahn, J. / Jo, I. / Hong, S. / Ryu, S. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kod.cif.gz | 430.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kod.ent.gz | 282.5 KB | Display | PDB format |
PDBx/mmJSON format | 6kod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kod_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6kod_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6kod_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 6kod_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/6kod ftp://data.pdbj.org/pub/pdb/validation_reports/ko/6kod | HTTPS FTP |
-Related structure data
Related structure data | 6kgySC 6kyyC S: Starting model for refinement C: citing same article (ref.) |
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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: 49020.754 Da / Num. of mol.: 4 / Mutation: C43S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Gene: ECBD_3354 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A140ND83, UniProt: P77212*PLUS #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-CL / | 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: 3.22 Å3/Da / Density % sol: 61.8 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.05 M Ammonium sulfate, 0.05 M Bis-Tris HCl (pH 5.8), 28 % pentaerythrytol ethoxylate (15/4_EO/OH), 5 mM CuSO4 |
-Data collection
Diffraction | Mean temperature: 100.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 45601 / % possible obs: 92.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 51.4 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.045 / Rrim(I) all: 0.098 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3→3.05 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2029 / CC1/2: 0.669 / Rpim(I) all: 0.163 / Rrim(I) all: 0.288 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KGY Resolution: 3→46.61 Å / SU ML: 0.3745 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 25.1906
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→46.61 Å
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Refine LS restraints |
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LS refinement shell |
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