+Open data
-Basic information
Entry | Database: PDB / ID: 5g5g | ||||||
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Title | Escherichia coli Periplasmic Aldehyde Oxidase | ||||||
Components | (PUTATIVE XANTHINE DEHYDROGENASE ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / PAOABC / XANTHINE OXIDASE FAMILY / HETEROTRIMER / E.COLI DETOXIFICATION | ||||||
Function / homology | Function and homology information 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 | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Correia, M.A.S. / Otrelo-Cardoso, A.R. / Romao, M.J. / Santos-Silva, T. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g5g.cif.gz | 494.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g5g.ent.gz | 400.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g5g_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5g5g_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5g5g_validation.xml.gz | 56.3 KB | Display | |
Data in CIF | 5g5g_validation.cif.gz | 83.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5g ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5g | HTTPS FTP |
-Related structure data
Related structure data | 5g5hC 1ffuS 1ffvS 1rm6S 1t3qS 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 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.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: P77165 |
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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.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: P77324 |
#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.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: P77489 |
-Non-polymers , 10 types, 1016 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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