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Yorodumi- PDB-4r6h: Crystal structure of putative binding protein msme from bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r6h | ||||||
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Title | Crystal structure of putative binding protein msme from bacillus subtilis subsp. subtilis str. 168, target efi-510764, an open conformation | ||||||
Components | Solute binding protein MsmE | ||||||
Keywords | TRANSPORT PROTEIN / SUGAR TRANSPORTER / SBP-TYPE / EFI / STRUCTURAL GENOMICS / Enzyme Function Initiative | ||||||
Function / homology | polysaccharide transport / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / plasma membrane / Alpha Beta / Melibiose/raffinose/stachyose-binding protein MelE Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Al obaidi, N. / Chamala, S. / Attonito, J.D. / Scott glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al obaidi, N. / Chamala, S. / Attonito, J.D. / Scott glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Transporter Msme from Bacillus Subtilis, Target Efi-510764 Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al obaidi, N. / Chamala, S. / Scott glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al obaidi, N. / Chamala, S. / Scott glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r6h.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r6h.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 4r6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/4r6h ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r6h | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48697.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: msmE, BSU30270 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34335 | ||
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#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4 Details: PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 5% GLYCEROL, 5 MM DTT; RESERVOIR: 1.0 M LITHIUM CHLORIDE, 0.1 M SODIUM CITRATE:HCL, PH 4.0, 20% PEG6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2014 / Details: MIRRORS |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→57.35 Å / Num. obs: 63410 / % possible obs: 98.4 % / Observed criterion σ(I): -5 / Redundancy: 6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / Rsym value: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→57.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.499 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.077 / 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: 26.932 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→57.35 Å
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