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Yorodumi- PDB-4rs3: Crystal structure of carbohydrate transporter A0QYB3 from Mycobac... -
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-Basic information
Entry | Database: PDB / ID: 4rs3 | ||||||
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Title | Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol | ||||||
Components | ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS / HYDROLASE | ||||||
Function / homology | Function and homology information cellular response to carbohydrate stimulus / carbohydrate transport / carbohydrate binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Siedel, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis. Authors: Huang, H. / Carter, M.S. / Vetting, M.W. / Al-Obaidi, N. / Patskovsky, Y. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rs3.cif.gz | 141.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rs3.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 4rs3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rs3_validation.pdf.gz | 468 KB | Display | wwPDB validaton report |
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Full document | 4rs3_full_validation.pdf.gz | 469.1 KB | Display | |
Data in XML | 4rs3_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 4rs3_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/4rs3 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/4rs3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 34605.309 Da / Num. of mol.: 1 / Fragment: residues 25-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3598, MSMEI_3515 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0QYB3, monosaccharide-transporting ATPase |
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#2: Sugar | ChemComp-XYL / |
-Non-polymers , 5 types, 263 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-IMD / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-ACT / #7: Water | ChemComp-HOH / | |
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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: 2.12 Å3/Da / Density % sol: 42.06 % |
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Crystal grow | pH: 7 Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM DL-XYLITOL), RESERVOIR: 0.1 M IMIDAZOLE-HCL, PH 8.0, 0.2M ZINC ACETATE, 2.5M SODIUM CHLORIDE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR ...Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM DL-XYLITOL), RESERVOIR: 0.1 M IMIDAZOLE-HCL, PH 8.0, 0.2M ZINC ACETATE, 2.5M SODIUM CHLORIDE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 24, 2014 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 57826 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 21.085 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.1 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→47.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.934 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.564 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→47.76 Å
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Refine LS restraints |
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