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- PDB-4z9r: Crystal structure of PfaD from Shewanella oneidensis in complex w... -
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Basic information
Entry | Database: PDB / ID: 4z9r | ||||||
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Title | Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction. | ||||||
![]() | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | ||||||
![]() | OXIDOREDUCTASE / PfaD / NAD+ / In-situ | ||||||
Function / homology | ![]() nitronate monooxygenase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baker, G.E. / Race, P.R. | ||||||
![]() | ![]() Title: Crystal structure of PfaD from Shewanella oneidensis in complex with NAD+ determined by in-situ diffraction. Authors: Baker, G.E. / Race, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.7 KB | Display | ![]() |
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PDB format | ![]() | 157.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 37 KB | Display | |
Data in CIF | ![]() | 49.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yx6S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 20 - 544 / Label seq-ID: 20 - 544
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Components
#1: Protein | Mass: 59670.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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: 2.59 Å3/Da / Density % sol: 52.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M potassium/sodium tartate, 0.1 M Bis tris propane at pH 8.5 and 20 % (w/v) polyethylene glycol. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.44 Å / Num. obs: 30357 / % possible obs: 95.9 % / Observed criterion σ(I): 9.6 / Redundancy: 4.7 % / Rmerge(I) obs: 0.278 / Net I/σ(I): 9.6 |
Reflection shell | Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 3.4 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YX6 Resolution: 2.8→48.44 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.871 / SU B: 15.415 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 32.51 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→48.44 Å
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Refine LS restraints |
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