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Yorodumi- PDB-6e13: Pseudomonas putida PqqB with a non-physiological zinc at the acti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 60000000000000 | |||||||||
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Title | Pseudomonas putida PqqB with a non-physiological zinc at the active site binds the substrate mimic, 5-cysteinyl-3,4-dihydroxyphenylalanine (5-Cys-DOPA), non-specifically but supports the proposed function of the enzyme in pyrroloquinoline quinone biosynthesis. | |||||||||
Components | Coenzyme PQQ synthesis protein B | |||||||||
Keywords | OXIDOREDUCTASE / iron-dependent / hydroxylase / metallo beta-lactamase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.349 Å | |||||||||
Authors | Evans III, R.L. / Wilmot, C.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway. Authors: Koehn, E.M. / Latham, J.A. / Armand, T. / Evans 3rd, R.L. / Tu, X. / Wilmot, C.M. / Iavarone, A.T. / Klinman, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e13.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e13.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 6e13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e13_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6e13_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6e13_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 6e13_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/6e13 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/6e13 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 33999.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria) Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pqqB, PP_0379 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88QV5, Oxidoreductases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-HKS / | #5: 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: 2.92 Å3/Da / Density % sol: 57.81 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 2.5 mg/mL PqqB, 50 mM sodium chloride, 10 mM Tris-HCl, pH 7.5 against reservoir solution for unliganded PqqB (11% PEG4000, 0.2 M sodium chloride, 80 uM zinc chloride, 0.1 M Bis-Tris, pH 6.7) |
-Data collection
Diffraction | Mean temperature: 295 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→50 Å / Num. obs: 17434 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.037 / Rrim(I) all: 0.13 / Χ2: 1.072 / Net I/σ(I): 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.349→45.472 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.25 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.7 Å2 / Biso mean: 44.0654 Å2 / Biso min: 18.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.349→45.472 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %
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