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Open data
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Basic information
Entry | Database: PDB / ID: 5g5g | ||||||
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Title | Escherichia coli Periplasmic Aldehyde Oxidase | ||||||
![]() | (PUTATIVE XANTHINE DEHYDROGENASE ...) x 3 | ||||||
![]() | OXIDOREDUCTASE / PAOABC / XANTHINE OXIDASE FAMILY / HETEROTRIMER / E.COLI DETOXIFICATION | ||||||
Function / homology | ![]() carboxylate reductase / carboxylate reductase activity / oxidoreductase activity, acting on the aldehyde or oxo group of donors / oxidoreductase complex / cellular detoxification of aldehyde / molybdenum ion binding / : / FAD binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding ...carboxylate reductase / carboxylate reductase activity / oxidoreductase activity, acting on the aldehyde or oxo group of donors / oxidoreductase complex / cellular detoxification of aldehyde / molybdenum ion binding / : / FAD binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / periplasmic space / oxidoreductase activity / iron ion binding / DNA damage response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Correia, M.A.S. / Otrelo-Cardoso, A.R. / Romao, M.J. / Santos-Silva, T. | ||||||
![]() | ![]() Title: The Escherichia Coli Periplasmic Aldehyde Oxidoreductase is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. Authors: Correia, M.A. / Otrelo-Cardoso, A.R. / Schwuchow, V. / Sigfridsson Clauss, K.G. / Haumann, M. / Romao, M.J. / Leimkuhler, S. / Santos-Silva, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 494.3 KB | Display | ![]() |
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PDB format | ![]() | 400.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 56.3 KB | Display | |
Data in CIF | ![]() | 83.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g5hC ![]() 1ffuS ![]() 1ffvS ![]() 1rm6S ![]() 1t3qS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-PUTATIVE XANTHINE DEHYDROGENASE ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 24370.664 Da / Num. of mol.: 1 Fragment: PERIPLASMIC ALDEHYDE OXIDASE ALPHA SUBUNIT, RESIDUES 1-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 33900.840 Da / Num. of mol.: 1 Fragment: PERIPLASMIC ALDEHYDE OXIDASE BETA SUBUNIT, RESIDUES 1-318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 78180.258 Da / Num. of mol.: 1 Fragment: PERIPLASMIC ALDEHYDE OXIDASE GAMMA SUBUNIT, RESIDUES 1-732 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 10 types, 1016 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MCN.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MCN.gif)
![](data/chem/img/MOS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-IOD / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-ACT / #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-SF4 / | #10: Chemical | ChemComp-FAD / | #11: Chemical | ChemComp-MCN / | #12: Chemical | ChemComp-MOS / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: PEG 3350, AMMONIUM IODIDE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.32 Å / Num. obs: 137342 / % possible obs: 98.5 % / Observed criterion σ(I): 1.9 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.9 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV Resolution: 1.7→48.32 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.426 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.871 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→48.32 Å
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Refine LS restraints |
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