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Yorodumi- PDB-2xd3: The crystal structure of MalX from Streptococcus pneumoniae in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xd3 | |||||||||
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Title | The crystal structure of MalX from Streptococcus pneumoniae in complex with maltopentaose. | |||||||||
Components | MALTOSE/MALTODEXTRIN-BINDING PROTEIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / SOLUTE-BINDING PROTEIN / VIRULENCE / ALPHA-GLUCAN / SUGAR TRANSPORT / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information maltoheptaose binding / maltodextrin transmembrane transporter activity / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / plasma membrane Similarity search - Function | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Abbott, D.W. / Higgins, M.A. / Hyrnuik, S. / Pluvinage, B. / Lammerts van Bueren, A. / Boraston, A.B. | |||||||||
Citation | Journal: Mol.Microbiol. / Year: 2010 Title: The Molecular Basis of Glycogen Breakdown and Transport in Streptococcus Pneumoniae. Authors: Abbott, D.W. / Higgins, M.A. / Hyrnuik, S. / Pluvinage, B. / Lammerts Van Bueren, A. / Boraston, A.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xd3.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xd3.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xd3_validation.pdf.gz | 899.8 KB | Display | wwPDB validaton report |
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Full document | 2xd3_full_validation.pdf.gz | 903.7 KB | Display | |
Data in XML | 2xd3_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 2xd3_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/2xd3 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xd3 | HTTPS FTP |
-Related structure data
Related structure data | 2xd2C 2ghaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44928.016 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PMALX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59213 | ||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | #4: 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: 2.53 Å3/Da / Density % sol: 51.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 29101 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.5 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GHA Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.959 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.18 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.078 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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