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Open data
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Basic information
Entry | Database: PDB / ID: 8gqr | ||||||
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Title | Crystal structure of VioD with FAD | ||||||
![]() | VioD | ||||||
![]() | FLAVOPROTEIN / complex | ||||||
Function / homology | FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / VioD![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ran, T. / Wang, W. / Xu, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for substrate binding and catalytic mechanism of the key enzyme VioD in the violacein synthesis pathway. Authors: Xu, M. / Xu, D. / Gao, M. / Zhuang, X. / Wang, W. / Sun, B. / Ran, 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 | ![]() | 174 KB | Display | ![]() |
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PDB format | ![]() | 132 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 979.5 KB | Display | ![]() |
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Full document | ![]() | 985.1 KB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 48.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h0mC ![]() 3c4aS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44543.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.77 Å / Num. obs: 49417 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.982 / Rpim(I) all: 0.13 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 3951 / CC1/2: 0.499 / Rpim(I) all: 0.677 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3C4A Resolution: 2.1→19.77 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 26.75 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.77 Å
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Refine LS restraints |
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