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- PDB-4wkb: 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: 4wkb | ||||||
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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 / hydrolase / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wkcC ![]() 4x24C ![]() 3dp9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26225.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A5F5R2, adenosylhomocysteine nucleosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.72 % / Description: Block |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Protein (10 mg/mL); Reservoir (0.1M di-ammonium hydrogen citrate and 15% PEG 3350); Cryoprotection (20% (v/v) glycerol) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.37→50 Å / Num. obs: 85031 / % possible obs: 93 % / Redundancy: 3.9 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.291 / Net I/av σ(I): 27.33 / Net I/σ(I): 16.2 / Num. measured all: 330001 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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: 1.37→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1978 / WRfactor Rwork: 0.1739 / FOM work R set: 0.8889 / SU B: 0.81 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0587 / SU Rfree: 0.0584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.058 / SU Rfree Cruickshank DPI: 0.0584 / 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: 40.33 Å2 / Biso mean: 13.758 Å2 / Biso min: 6.51 Å2
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Refinement step | Cycle: final / Resolution: 1.37→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Total num. of bins used: 20
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