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Yorodumi- PDB-7cba: Crystal structure of snake venom phosphodiesterase (PDE) from Tai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cba | ||||||
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Title | Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with isorhamnetin and citrate | ||||||
Components | Venom phosphodiesterase | ||||||
Keywords | HYDROLASE / ATP-hydrolysis glycoprotein enpp inhibitor | ||||||
Function / homology | Function and homology information ADP phosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / toxin activity / nucleic acid binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Naja atra (Chinese cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.901 Å | ||||||
Authors | Lin, I.J. / Lin, C.C. / Wu, W.G. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: To Be Published Title: Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with isorhamnetin and citrate Authors: Lin, I.J. / Lin, C.C. / Wu, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cba.cif.gz | 318.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cba.ent.gz | 263.8 KB | Display | PDB format |
PDBx/mmJSON format | 7cba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/7cba ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cba | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-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:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 94728.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) References: UniProt: A0A2D0TC04, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Sugars , 2 types, 9 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 10 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | #7: Chemical | |
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-Details
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: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Ammonium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99984 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 25, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→30 Å / Num. obs: 42715 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.059 / Rrim(I) all: 0.112 / Χ2: 0.851 / Net I/σ(I): 7.4 / Num. measured all: 153134 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.901→28.296 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.82 / 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: 113.14 Å2 / Biso mean: 48.2364 Å2 / Biso min: 17.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.901→28.296 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
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