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- PDB-6f73: Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f73 | |||||||||
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Title | Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora thermophila C1 | |||||||||
![]() | MtVAO615 | |||||||||
![]() | FLAVOPROTEIN / VAO-type / FAD | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rozeboom, H.J. / Fraaije, M.W. | |||||||||
![]() | ![]() Title: Characterization of Two VAO-Type Flavoprotein Oxidases from Myceliophthora thermophila. Authors: Ferrari, A.R. / Rozeboom, H.J. / Vugts, A.S.C. / Koetsier, M.J. / Floor, R. / Fraaije, M.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 451.6 KB | Display | ![]() |
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PDB format | ![]() | 369.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 71.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f72C ![]() 6f74C ![]() 2bvfS ![]() 2ipiS ![]() 2y08S ![]() 3rj8S ![]() 3w8wS C: citing same article ( 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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1 | ![]()
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2 | ![]()
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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: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 27 - 574 / Label seq-ID: 27 - 574
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Components
#1: Protein | Mass: 62024.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: First 17 residues are a signal sequence Source: (gene. exp.) ![]() Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2305637 Production host: ![]() References: UniProt: G2QDQ9 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG6000, , 0.2 M NaCl, 0.1 M NaAcetate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 2015 |
Radiation | Monochromator: Helios MX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→58 Å / Num. obs: 71982 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.081 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.22→2.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4265 / CC1/2: 0.706 / Rpim(I) all: 0.225 / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IPI, 2BVF, 2Y08, 3W8W,3RJ8 Resolution: 2.22→58 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.198 / 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.81 Å2
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Refinement step | Cycle: 1 / Resolution: 2.22→58 Å
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Refine LS restraints |
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