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- PDB-1z42: Crystal structure of oxidized YqjM from Bacillus subtilis complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1z42 | ||||||
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Title | Crystal structure of oxidized YqjM from Bacillus subtilis complexed with p-hydroxybenzaldehyde | ||||||
![]() | Probable NADH-dependent flavin oxidoreductase yqjM | ||||||
![]() | OXIDOREDUCTASE / flavin / FMN / p-hydroxybenzaldehyde / beta-alpha-barrel | ||||||
Function / homology | ![]() NADPH dehydrogenase / : / NADPH dehydrogenase activity / response to toxic substance / FMN binding / NADP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kitzing, K. / Fitzpatrick, T.B. / Wilken, C. / Sawa, J. / Bourenkov, G.P. / Macheroux, P. / Clausen, T. | ||||||
![]() | ![]() Title: The 1.3 A Crystal Structure of the Flavoprotein YqjM Reveals a Novel Class of Old Yellow Enzymes Authors: Kitzing, K. / Fitzpatrick, T.B. / Wilken, C. / Sawa, J. / Bourenkov, G.P. / Macheroux, P. / Clausen, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.6 KB | Display | ![]() |
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PDB format | ![]() | 127.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 49.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, y, -z+0.5 |
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Components
#1: Protein | Mass: 38146.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris/HCl, PEG 3500, lithium sulfate, strontium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 3, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→10 Å / Num. all: 180405 / Num. obs: 66570 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.71 % / Rsym value: 0.085 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.65 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 3211 / Rsym value: 0.221 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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