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- PDB-4x24: Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-ade... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x24 | ||||||
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Title | Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-DADMe-Immucillin-A | ||||||
![]() | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | ||||||
![]() | hydrolase/hydrolase inhibitor / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Cameron, S.A. / Thomas, K. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Active site and remote contributions to catalysis in methylthioadenosine nucleosidases. Authors: Thomas, K. / Cameron, S.A. / Almo, S.C. / Burgos, E.S. / Gulab, S.A. / Schramm, V.L. #1: ![]() Title: Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing Authors: Gutierrez, J.A. / Crowder, T. / Rinaldo-Matthis, A. / Ho, M.-C. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.4 KB | Display | ![]() |
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PDB format | ![]() | 83.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wkbC ![]() 4wkcC ![]() 3dp9S 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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Unit cell |
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Components
#1: Protein | Mass: 26165.822 Da / Num. of mol.: 2 / Mutation: A113P, V153I, R158G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: mtnN, pfs, VC0395_A1957, VC395_2494 / Plasmid: pDEST14 / Production host: ![]() ![]() ![]() References: UniProt: A5F5R2, ![]() #2: Chemical | #3: Chemical | ChemComp-PGE / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.15 % / Description: rods |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: Protein (10 mg/mL); Reservoir (0.2M ammonium chloride pH 6.3 and 20% PEG 3350); Cryoprotection (20% (v/v) glycerol) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 9, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 69602 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.337 / Net I/av σ(I): 18.68 / Net I/σ(I): 8.9 / Num. measured all: 253993 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3DP9 Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1856 / WRfactor Rwork: 0.1673 / FOM work R set: 0.8571 / SU B: 1.418 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0724 / SU Rfree: 0.0699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.07 / SU Rfree Cruickshank DPI: 0.0699 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.04 Å2 / Biso mean: 17.318 Å2 / Biso min: 8.77 Å2
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Refinement step | Cycle: final / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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