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Yorodumi- PDB-3jxp: Crystal Structure of the Coenzyme PQQ Synthesis Protein (PqqB) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jxp | ||||||
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Title | Crystal Structure of the Coenzyme PQQ Synthesis Protein (PqqB) from Pseudomonas putida | ||||||
Components | Coenzyme PQQ synthesis protein B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / alpha-beta protein / pqq biosynthesis / Transport | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Metlitzky, M. / Schwarzenbacher, R. | ||||||
Citation | Journal: J. Biophys. Chem. / Year: 2012 Title: Crystal structure of PqqB from Pseudomonas putida at 2.2 A resolution Authors: Metlitzky, M. / Puehringer, S. / Fisher, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jxp.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jxp.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 3jxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/3jxp ftp://data.pdbj.org/pub/pdb/validation_reports/jx/3jxp | HTTPS FTP |
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-Related structure data
Related structure data | 1xtoS 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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2 |
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Unit cell |
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Details | monomer |
-Components
#1: Protein | Mass: 35740.426 Da / Num. of mol.: 1 / Mutation: M253T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_0379, pqqB / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(de3)Star / References: UniProt: Q88QV5 | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: 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: 2.84 Å3/Da / Density % sol: 56.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M TRIS hydrochloride pH 8.5, 0.2 M Magnesium chloride hexahydrate, 15% w/v PEG 4,000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 18, 2009 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→67.7 Å / Num. all: 21579 / Num. obs: 21411 / % possible obs: 98.2 % |
Reflection shell | Resolution: 2.2→2.257 Å / Rmerge(I) obs: 0.569 / % possible all: 99.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XTO Resolution: 2.2→67.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.926 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.329 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→67.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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