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Yorodumi- PDB-5g60: S.pneumoniae ABC-transporter substrate binding protein FusA in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g60 | |||||||||
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Title | S.pneumoniae ABC-transporter substrate binding protein FusA in complex with nystose | |||||||||
Components | ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN | |||||||||
Keywords | TRANSPORT PROTEIN / FUSA / SUBSTRATE-BINDING-PROTEIN / ABC-TRANSPORTER / TRANSPORTER / FRUCTOOLIGOSACCHARIDES / KESTOSE / NYSTOSE / FRUCTO-NYSTOSE / CARBOHYDRATE / SUGAR / TRANSPORT / PNEUMONIAE | |||||||||
Function / homology | polysaccharide transport / : / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / plasma membrane / nystose / Fructooligosaccharide ABC transporter substrate-binding protein FusA Function and homology information | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | |||||||||
Authors | Culurgioni, S. / Harris, G. / Singh, A.K. / King, S.J. / Walsh, M.A. | |||||||||
Citation | Journal: Structure / Year: 2017 Title: Structural Basis for Regulation and Specificity of Fructooligosaccharide Import in Streptococcus pneumoniae. Authors: Culurgioni, S. / Harris, G. / Singh, A.K. / King, S.J. / Walsh, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g60.cif.gz | 430.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g60.ent.gz | 353.4 KB | Display | PDB format |
PDBx/mmJSON format | 5g60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g60_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5g60_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5g60_validation.xml.gz | 83.9 KB | Display | |
Data in CIF | 5g60_validation.cif.gz | 126.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/5g60 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/5g60 | HTTPS FTP |
-Related structure data
Related structure data | 5g5ySC 5g5zC 5g61C 5g62C S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 56350.738 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: A0A0H2URD6 #2: Polysaccharide | beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / nystose |
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-Non-polymers , 4 types, 1663 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | LACKING THE FIRST 47 N-TERMINAL AMINOACIDS |
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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 8 Details: 20 % PEG6000, 0.1M SODIUM ACETATE PH 5.0, 0.02 M CALCIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2014 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→57.37 Å / Num. obs: 144038 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.1 / % possible all: 77.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5G5Y Resolution: 1.99→119.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.45 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.162 / 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 mean: 29.493 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→119.54 Å
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Refine LS restraints |
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