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- PDB-6m53: Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m53 | ||||||
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Title | Crystal structure of 2, 3-dihydroxybenzoic acid decarboxylase from Fusarium oxysporum | ||||||
![]() | 2,3-dihydroxybenzoate decarboxylase | ||||||
![]() | BIOSYNTHETIC PROTEIN / 2 / 3-dihydroxybenzoic acid decarboxylase | ||||||
Function / homology | ![]() secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, M.K. / Feng, J.H. / Liu, W.D. / Wu, Q.Q. / Zhu, D.M. | ||||||
![]() | ![]() Title: 2,3-Dihydroxybenzoic Acid Decarboxylase from Fusarium oxysporum: Crystal Structures and Substrate Recognition Mechanism. Authors: Song, M. / Zhang, X. / Liu, W. / Feng, J. / Cui, Y. / Yao, P. / Wang, M. / Guo, R.T. / Wu, Q. / Zhu, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311 KB | Display | ![]() |
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PDB format | ![]() | 247.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 97.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bp1C ![]() 7bpcC ![]() 2dvtS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 39290.387 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.42 % / Mosaicity: 0.415 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 mol/L tri-potassium citrate, 20% (w/v) PEG 3350 and 10% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 26, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→25 Å / Num. obs: 207763 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.022 / Rrim(I) all: 0.044 / Χ2: 1.589 / Net I/σ(I): 16.2 / Num. measured all: 796743 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DVT Resolution: 1.55→24.77 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.99 Å2 / Biso mean: 26.3993 Å2 / Biso min: 11.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→24.77 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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