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Yorodumi- PDB-3hnh: Crystal Structure of PqqC Active Site Mutant Y175S,R179S in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hnh | ||||||
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Title | Crystal Structure of PqqC Active Site Mutant Y175S,R179S in complex with a reaction intermediate | ||||||
Components | Pyrroloquinoline-quinone synthase | ||||||
Keywords | OXIDOREDUCTASE / PqqC / PQQ biosynthesis / oxidase / complex / all helical | ||||||
Function / homology | Function and homology information pyrroloquinoline-quinone synthase activity / pyrroloquinoline-quinone synthase / pyrroloquinoline quinone biosynthetic process / sulfur compound metabolic process / : Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Puehringer, S. / Schwarzenbacher, R. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Structural studies of mutant forms of the PQQ-forming enzyme PqqC in the presence of product and substrate Authors: Puehringer, S. / RoseFigura, J. / Metlitzky, M. / Toyama, H. / Klinman, J.P. / Schwarzenbacher, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hnh.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hnh.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hnh_validation.pdf.gz | 799.4 KB | Display | wwPDB validaton report |
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Full document | 3hnh_full_validation.pdf.gz | 804.7 KB | Display | |
Data in XML | 3hnh_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 3hnh_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/3hnh ftp://data.pdbj.org/pub/pdb/validation_reports/hn/3hnh | HTTPS FTP |
-Related structure data
Related structure data | 3hlxC 3hmlC 1otvS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 29856.707 Da / Num. of mol.: 1 / Mutation: Y175S, R179S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: MGH 78578 / Gene: PqqC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A6T9H1, pyrroloquinoline-quinone synthase |
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#2: Chemical | ChemComp-AHQ / ( |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE LIGAND LABELED AS AHQ IN THIS ENTRY IS UNDER TRANSITION. IT IS UNIDENTIFIED REACTION ...THE LIGAND LABELED AS AHQ IN THIS ENTRY IS UNDER TRANSITION |
-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: 48.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium chloride, 0.1M Tris pH 8.5, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 7, 2008 | ||||||||||||||||||||||||
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→49.629 Å / Num. obs: 26201 / % possible obs: 97.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.066 / Net I/σ(I): 13.7 / Num. measured all: 118953 | ||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OTV Resolution: 1.8→49.629 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.869 / SU B: 5.428 / SU ML: 0.084 / SU R Cruickshank DPI: 0.123 / SU Rfree: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; unidentified density next to C5 of AHQ, ARG80 and NE2 of HIS84.
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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 max: 73.12 Å2 / Biso mean: 44.854 Å2 / Biso min: 25.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→49.629 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -3.114 Å / Origin y: -40.206 Å / Origin z: -13.145 Å / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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