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Yorodumi- PDB-4rsm: Crystal structure of carbohydrate transporter msmeg_3599 from myc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rsm | ||||||
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Title | Crystal structure of carbohydrate transporter msmeg_3599 from mycobacterium smegmatis str. mc2 155, target efi-510970, in complex with d-threitol | ||||||
Components | Periplasmic binding protein/LacI transcriptional regulator | ||||||
Keywords | TRANSPORT PROTEIN / SUGAR TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS / HYDROLASE | ||||||
Function / homology | Function and homology information carbohydrate utilization / cellular response to carbohydrate stimulus / carbohydrate transport / carbohydrate binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 | 4rsm.cif.gz | 485.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rsm.ent.gz | 401.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/4rsm ftp://data.pdbj.org/pub/pdb/validation_reports/rs/4rsm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34346.574 Da / Num. of mol.: 4 / Fragment: UNP residues 25-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3599, MSMEI_3516 / Plasmid: pet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QYB5 #2: Chemical | ChemComp-3VB / #3: 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: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-THREITOL), RESERVOIR: 0.1 M CITRIC ACID:NAOH, PH 4.0, 25% PEG3350, 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: 1.6→50 Å / Num. obs: 126794 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.5 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.948 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.245 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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