+Open data
-Basic information
Entry | Database: PDB / ID: 5g5h | |||||||||
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Title | Escherichia coli Periplasmic Aldehyde Oxidase R440H mutant | |||||||||
Components | (Aldehyde oxidoreductase ...) 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 K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 5g5h.cif.gz | 480.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g5h.ent.gz | 388 KB | Display | PDB format |
PDBx/mmJSON format | 5g5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5h ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5h | HTTPS FTP |
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-Related structure data
Related structure data | 5g5gC 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
-Aldehyde oxidoreductase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 24370.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: paoA, yagT, b0286, JW0280 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI TP1000 / References: UniProt: P77165, carboxylate reductase |
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#2: Protein | Mass: 33900.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: paoB, yagS, b0285, JW0279 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI TP1000 / References: UniProt: P77324, carboxylate reductase |
#3: Protein | Mass: 78161.203 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: paoC, yagR, b0284, JW0278 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI TP1000 / References: UniProt: P77489, carboxylate reductase |
-Non-polymers , 10 types, 691 molecules
#4: Chemical | #5: Chemical | ChemComp-IOD / #6: Chemical | #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-SF4 / | #9: Chemical | ChemComp-FAD / | #10: Chemical | ChemComp-MCN / | #11: Chemical | ChemComp-MOS / | #12: Chemical | #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: 48.55 % / 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: ESRF / Beamline: BM14 / Wavelength: 0.979 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.27 Å / Num. obs: 55360 / % possible obs: 98 % / Observed criterion σ(I): 1.81 / Redundancy: 7.2 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.81 / % possible all: 84.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV Resolution: 2.3→48.27 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.892 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.324 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.27 Å
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Refine LS restraints |
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