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Yorodumi- PDB-4o5q: Crystal Structure of the Alkylhydroperoxide Reductase AhpF from E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o5q | ||||||
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Title | Crystal Structure of the Alkylhydroperoxide Reductase AhpF from Escherichia coli | ||||||
Components | Alkyl hydroperoxide reductase subunit F | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information alkyl hydroperoxide reductase complex / Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / alkyl hydroperoxide reductase activity / thioredoxin-disulfide reductase (NADPH) activity / FAD binding / cell redox homeostasis / response to reactive oxygen species / hydrogen peroxide catabolic process / NAD binding / response to oxidative stress / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Dip, P.V. / Kamariah, N. / Manimekalai, M.S.S. / Balakrishna, A.M. / Gruber, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli Authors: Dip, P.V. / Kamariah, N. / Subramanian Manimekalai, M.S. / Nartey, W. / Balakrishna, A.M. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G. #1: Journal: J.Mol.Biol. / Year: 2010 Title: Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli Authors: Bieger, B. / Essen, L.O. #2: Journal: Biochemistry / Year: 2001 Title: Structure of intact AhpF reveals a mirrored thioredoxin-like active site and implies large domain rotations during catalysis Authors: Wood, Z.A. / Poole, L.B. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o5q.cif.gz | 323.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o5q.ent.gz | 265.9 KB | Display | PDB format |
PDBx/mmJSON format | 4o5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/4o5q ftp://data.pdbj.org/pub/pdb/validation_reports/o5/4o5q | HTTPS FTP |
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-Related structure data
Related structure data | 4o5rC 4o5uC 1hyuS C: citing same article (ref.) 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56242.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P35340 |
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-Non-polymers , 8 types, 528 molecules
#2: Chemical | ChemComp-FAD / | ||||||||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PGE / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CD / | #7: Chemical | ChemComp-PG4 / | #8: Chemical | ChemComp-TRS / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.74 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 0.1M Na-Hepes, 2.5%(v/v) PEG400, 2M ammonium sulfate, 10mM cadmium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2012 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7.3 % / Number: 346921 / Rmerge(I) obs: 0.067 / Χ2: 0.53 / D res high: 2 Å / D res low: 30 Å / Num. obs: 47455 / % possible obs: 99.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2→30 Å / Num. obs: 47454 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.1 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HYU Resolution: 2→26.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.19 / Isotropic thermal model: Isotropic / σ(F): 1.38 / Phase error: 17.09 / Stereochemistry target values: ML Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2→26.62 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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