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- PDB-4gi5: Crystal Structure Of a Putative quinone reductase from Klebsiella... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gi5 | ||||||
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Title | Crystal Structure Of a Putative quinone reductase from Klebsiella pneumoniae (Target PSI-013613) | ||||||
![]() | quinone reductase | ||||||
![]() | OXIDOREDUCTASE / Quinone reductase / Protein structure initiative / FAD bound / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. ...Kumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Washington, E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
![]() | ![]() Title: Crystal structure of a quinone reductase from Klebsiella pneumoniae with bound FAD Authors: Kumar, P.R. / Hillerich, B. / Love, J. / Seidel, R. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.1 KB | Display | ![]() |
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PDB format | ![]() | 106.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1017.8 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a dimer |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31976.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MGH 78578 / Gene: KPN78578_46790, KPN_04757 / Plasmid: pSGC / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 446 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M NA2HPO4/KH2PO4, PH 6.2, 2.5M NACL - MCSG3 #6); Cryoprotection (Glycerol), Sitting Drop, Vapor Diffusion, temperature ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M NA2HPO4/KH2PO4, PH 6.2, 2.5M NACL - MCSG3 #6); Cryoprotection (Glycerol), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2011 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 194318 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.086 / Χ2: 1.542 / Net I/σ(I): 26.8979 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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Processing
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Refinement | Method to determine structure: ![]() Details: A VERY LARGE POSITIVE DENSITY WAS SEEN ADJACENT TO THE FAD LIGANDS IN BOTH PROTEIN MONOMERS. THIS WAS INITIALLY MODELLED AS A BENZOIC ACID LIGAND (BEZ). THE EXACT IDENTITY OF THE ACTUAL ...Details: A VERY LARGE POSITIVE DENSITY WAS SEEN ADJACENT TO THE FAD LIGANDS IN BOTH PROTEIN MONOMERS. THIS WAS INITIALLY MODELLED AS A BENZOIC ACID LIGAND (BEZ). THE EXACT IDENTITY OF THE ACTUAL LIGAND IN THE STRUCTURE IS UNKNOWN. IT IS A POSSIBLE EXPRESSION ARTIFACT AND HAS BEEN DENOTED AS UNKNOWN LIGAND (UNL). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 91.57 Å2 / Biso mean: 22.1059 Å2 / Biso min: 10.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→48.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.752→1.798 Å / Total num. of bins used: 20
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