+Open data
-Basic information
Entry | Database: PDB / ID: 5ffq | ||||||
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Title | ChuY: An Anaerobillin Reductase from Escherichia coli O157:H7 | ||||||
Components | ShuY-like protein | ||||||
Keywords | UNKNOWN FUNCTION / NADPH oxidoreductase | ||||||
Function / homology | NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily / 1,4-BUTANEDIOL / PHOSPHATE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | LaMattina, J.W. / Reedy, A.N. / Uy, K.G. / Lanzilotta, W.N. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Radical new paradigm for heme degradation in Escherichia coli O157:H7. Authors: LaMattina, J.W. / Nix, D.B. / Lanzilotta, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ffq.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ffq.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ffq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ffq_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 5ffq_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 5ffq_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 5ffq_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/5ffq ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ffq | HTTPS FTP |
-Related structure data
Related structure data | 3qvoS 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: 21835.865 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: chuY, ECs4385, Z4917 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8X5N4 #2: Chemical | #3: Chemical | ChemComp-BU1 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Bis Tris pH 5.6, 0.2 M Lithium Sulfate, 18% PEG 3350, 10% 1,4 Butanediol |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.4 Å / Num. obs: 27184 / % possible obs: 99.74 % / Redundancy: 2 % / Net I/σ(I): 2.82 |
Reflection shell | % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3qvo Resolution: 2→38.4 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6 / 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: 2→38.4 Å
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Refine LS restraints |
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LS refinement shell |
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