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Yorodumi- PDB-8h41: Crystal structure of a decarboxylase from Trichosporon moniliifor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h41 | ||||||
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Title | Crystal structure of a decarboxylase from Trichosporon moniliiforme in complex with o-nitrophenol | ||||||
Components | Salicylate decarboxylase | ||||||
Keywords | HYDROLASE / decarboxylase | ||||||
Function / homology | Function and homology information salicylate decarboxylase / organic substance metabolic process / carboxy-lyase activity / hydrolase activity Similarity search - Function | ||||||
Biological species | Cutaneotrichosporon moniliiforme (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Gao, J. / Zhao, Y.P. / Li, Q. / Liu, W.D. / Sheng, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Catalysts / Year: 2022 Title: A Combined Computational-Experimental Study on the Substrate Binding and Reaction Mechanism of Salicylic Acid Decarboxylase Authors: Chen, F. / Zhao, Y. / Zhang, C. / Wang, W. / Gao, J. / Li, Q. / Qin, H. / Dai, Y. / Liu, W. / Liu, F. / Su, H. / Sheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h41.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h41.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 8h41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/8h41 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/8h41 | HTTPS FTP |
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-Related structure data
Related structure data | 6jqwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 40986.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cutaneotrichosporon moniliiforme (fungus) Gene: sdc / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CT50, salicylate decarboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.1 Å3/Da / Density % sol: 41.37 % / Mosaicity: 1.247 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% w/v Poly(acrylic acid sodium salt) 5100, 0.02 M MgCl2, 0.1 M HEPES pH 7.5, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.78→30 Å / Num. obs: 64395 / % possible obs: 96.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 17.05 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Χ2: 1.873 / Net I/σ(I): 12.9 / Num. measured all: 382838 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JQW Resolution: 1.78→29.93 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.92 Å2 / Biso mean: 19.0955 Å2 / Biso min: 7.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.78→29.93 Å
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Refine LS restraints NCS |
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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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