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- PDB-4wkp: Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wkp | ||||||
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Title | Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with 2-(2-hydroxyethoxy)ethylthiomethyl-DADMe-Immucillin-A | ||||||
![]() | Aminodeoxyfutalosine nucleosidase | ||||||
![]() | hydrolase/hydrolase inhibitor / hydrolase / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | ![]() aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / menaquinone biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Cameron, S.A. / Wang, S. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: New Antibiotic Candidates against Helicobacter pylori. Authors: Wang, S. / Cameron, S.A. / Clinch, K. / Evans, G.B. / Wu, Z. / Schramm, V.L. / Tyler, P.C. #1: ![]() Title: A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori. Authors: Wang, S. / Haapalainen, A.M. / Yan, F. / Du, Q. / Tyler, P.C. / Evans, G.B. / Rinaldo-Matthis, A. / Brown, R.L. / Norris, G.E. / 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 | ![]() | 205.1 KB | Display | ![]() |
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PDB format | ![]() | 162 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wknC ![]() 4wkoC ![]() 4ynbC ![]() 4yo8C ![]() 4ffsS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26886.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9ZMY2, adenosylhomocysteine nucleosidase #2: Chemical | ChemComp-3QA / ( #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % / Description: Rods |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Protein (10 mg/mL); Reservoir (0.2 M sodium fluoride and 2.2 M ammonium sulfate); 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: Jun 20, 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: 1.58→50 Å / Num. obs: 128267 / % possible obs: 98.4 % / Redundancy: 7.8 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.107 / Χ2: 1.28 / Net I/av σ(I): 22.714 / Net I/σ(I): 7.8 / Num. measured all: 1005870 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 4FFS Resolution: 1.58→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2015 / WRfactor Rwork: 0.1739 / FOM work R set: 0.848 / SU B: 1.619 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0882 / SU Rfree: 0.0878 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / SU Rfree Cruickshank DPI: 0.0878 / 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: 51.31 Å2 / Biso mean: 15.966 Å2 / Biso min: 7.37 Å2
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Refinement step | Cycle: final / Resolution: 1.58→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.584→1.625 Å / Total num. of bins used: 20
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