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Yorodumi- PDB-6dqi: Crystal structure of SsuE FMN reductase Y118A mutant in apo form. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dqi | |||||||||
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Title | Crystal structure of SsuE FMN reductase Y118A mutant in apo form. | |||||||||
Components | FMN reductase (NADPH) | |||||||||
Keywords | FLAVOPROTEIN / OXIDOREDUCTASE / Reductase / FMN / NAD(P)H | |||||||||
Function / homology | Function and homology information FMN reductase complex / FMN reductase (NADPH) / cellular response to sulfate starvation / alkanesulfonate catabolic process / FMN reductase (NAD(P)H) activity / FMN reductase (NADPH) activity / DNA damage response / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | McFarlane, J.S. / Ellis, H.R. / Lamb, A.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Sci. / Year: 2019 Title: Not as easy as pi : An insertional residue does not explain the pi-helix gain-of-function in two-component FMN reductases. Authors: McFarlane, J.S. / Hagen, R.A. / Chilton, A.S. / Forbes, D.L. / Lamb, A.L. / Ellis, H.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dqi.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dqi.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 6dqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dqi_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 6dqi_full_validation.pdf.gz | 442.8 KB | Display | |
Data in XML | 6dqi_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 6dqi_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/6dqi ftp://data.pdbj.org/pub/pdb/validation_reports/dq/6dqi | HTTPS FTP |
-Related structure data
Related structure data | 6dqoC 6dqpC 4ptyS 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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Unit cell |
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-Components
#1: Protein | Mass: 21186.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ssuE, ycbP, b0937, JW0920 / Production host: Escherichia coli (E. coli) / References: UniProt: P80644, FMN reductase (NADPH) #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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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: 1.83 Å3/Da / Density % sol: 32.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris HCl pH 8.5 and 800 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38.707 Å / Num. obs: 23620 / % possible obs: 97.7 % / Redundancy: 7.4 % / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.95→2 Å / Mean I/σ(I) obs: 7 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4pty Resolution: 1.95→38.707 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→38.707 Å
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Refine LS restraints |
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LS refinement shell |
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