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- PDB-2cdu: The Crystal Structure of Water-forming NAD(P)H Oxidase from Lacto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cdu | |||||||||
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Title | The Crystal Structure of Water-forming NAD(P)H Oxidase from Lactobacillus sanfranciscensis | |||||||||
![]() | NADPH OXIDASE | |||||||||
![]() | OXIDOREDUCTASE / NAD(P)H OXIDASE / FLAVOENZYME | |||||||||
Function / homology | ![]() cell redox homeostasis / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lountos, G.T. / Jiang, R. / Wellborn, W.B. / Thaler, T.L. / Bommarius, A.S. / Orville, A.M. | |||||||||
![]() | ![]() Title: The Crystal Structure of Nad(P)H Oxidase from Lactobacillus Sanfranciscensis: Insights Into the Conversion of O(2) Into Two Water Molecules by the Flavoenzyme. Authors: Lountos, G.T. / Jiang, R. / Wellborn, W.B. / Thaler, T.L. / Bommarius, A.S. / Orville, A.M. #1: Journal: Acta Crsytallogr, Sect D / Year: 2004 Title: Crystallization and Preliminary Analysis of a Water-Forming Nadh Oxidase from Lactobacillus Sanfranciscensis Authors: Lountos, G.T. / Riebel, B.R. / Wellborn, W.B. / Bommarius, A.S. / Orville, A.M. #2: ![]() Title: Cofactor Regeneration of Both Nad from Nadh and Nadp from Nadph: Nadh Oxidase from Lactobacillus Sanfranciscensis Authors: Riebel, B.R. / Gibbs, P.R. / Wellborn, W.B. / Bommarius, A.S. #3: ![]() Title: Cofactor Regeneration of Nad from Nadh: Novel Water-Forming Nadh Oxidases Authors: Riebel, B.R. / Gibbs, P.R. / Wellborn, W.B. / Bommarius, A.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.7 KB | Display | ![]() |
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PDB format | ![]() | 161.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1f8wS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49720.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PKK223-3 / Production host: ![]() ![]() References: UniProt: Q9F1X5, Oxidoreductases; Acting on NADH or NADPH #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | pH: 7 Details: 10 MG/ML PROTEIN, 100MM HEPES PH 7.0, 18% W/V PEG 4000, 8% V/V 2-PROPANOL, 20 MM DITHIOTHREITOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9997 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.4 Å / Num. obs: 81507 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / % possible all: 73.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F8W Resolution: 1.8→81.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.176 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A 452, B 450, B451, B452 WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→81.65 Å
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Refine LS restraints |
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