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Yorodumi- PDB-5g5y: S.pneumoniae ABC-transporter substrate binding protein FusA apo s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g5y | ||||||
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Title | S.pneumoniae ABC-transporter substrate binding protein FusA apo structure | ||||||
Components | ABC TRANSPORTER, SUBSTRATE-BINDING PROTEINATP-binding cassette transporter | ||||||
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 / Fructooligosaccharide ABC transporter substrate-binding protein FusA Function and homology information | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 | 5g5y.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g5y.ent.gz | 194.8 KB | Display | PDB format |
PDBx/mmJSON format | 5g5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g5y ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g5y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0723, -0.9974, 0.002), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56350.738 Da / Num. of mol.: 2 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 |
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-Non-polymers , 5 types, 1300 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | GENE NAME SP_1796 LACKING THE FIST 47 N-TERMINAL RESIDUES, PLUS GP RESIDUE ADDITION AFTER 3C PROTEASE CUT |
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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: 3.05 Å3/Da / Density % sol: 59.72 % Description: A PARTIAL MODEL OF FUSA WAS OBTAINED BY FUSA-GFP CRYSTALS USING GFP AS STARTING MODEL FOR MOLECULAR REPLACEMENT |
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Crystal grow | pH: 8 Details: 15 % PEG6000, 0.1M TRIS-HCL PH 8.0, 0.01 M ZINC CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2552 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2552 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→68.01 Å / Num. obs: 114100 / % possible obs: 83.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.73→1.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.6 / % possible all: 33.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→70.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.422 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / 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: 24.943 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→70.76 Å
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Refine LS restraints |
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