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Yorodumi- PDB-2cdu: The Crystal Structure of Water-forming NAD(P)H Oxidase from Lacto... -
+Open data
-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 | |||||||||
Components | NADPH OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / NAD(P)H OXIDASE / FLAVOENZYME | |||||||||
Function / homology | Function and homology information cell redox homeostasis / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | |||||||||
Biological species | LACTOBACILLUS SANFRANCISCENSIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Lountos, G.T. / Jiang, R. / Wellborn, W.B. / Thaler, T.L. / Bommarius, A.S. / Orville, A.M. | |||||||||
Citation | Journal: Biochemistry / Year: 2006 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: Journal: Adv.Synth.Catal. / Year: 2003 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: Journal: Adv.Synth.Catal. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdu.cif.gz | 202.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdu.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cdu_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2cdu_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2cdu_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 2cdu_validation.cif.gz | 62.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdu ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdu | HTTPS FTP |
-Related structure data
Related structure data | 1f8wS 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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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.) LACTOBACILLUS SANFRANCISCENSIS (bacteria) Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9997 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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