+Open data
-Basic information
Entry | Database: PDB / ID: 2qw1 | ||||||
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Title | Glucose/galactose binding protein bound to 3-O-methyl D-glucose | ||||||
Components | D-galactose-binding periplasmic protein | ||||||
Keywords | TRANSPORT PROTEIN / PERIPLASMIC BINDING PROTEIN / ANTAGONIST / CHEMOTAXIS / TRANSPORT / GGBP / 3-O-METHYL GLUCOSE / Sugar transport | ||||||
Function / homology | Function and homology information methylgalactoside transport / galactose transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chemotaxis / outer membrane-bounded periplasmic space / carbohydrate binding / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Borrok, M.J. / Kiessling, L.L. / Forest, K.T. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2009 Title: Structure-based design of a periplasmic binding protein antagonist that prevents domain closure. Authors: Borrok, M.J. / Zhu, Y. / Forest, K.T. / Kiessling, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qw1.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qw1.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/2qw1 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/2qw1 | HTTPS FTP |
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-Related structure data
Related structure data | 2fw0S 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: 33407.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mglB / Plasmid: pVB2 / Production host: Escherichia coli (E. coli) / Strain (production host): HB929 / References: UniProt: P0AEE5 | ||
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#2: Sugar | ChemComp-3MG / | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | #5: 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: 3.5 Å3/Da / Density % sol: 64.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.0 M ammonium sulfate and 0.05 M sodium citrate dehydrate, 3-O-methyl glucose (5mM) was soaked in. 2.5 M Na Malonate cryoprotectant, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 25, 2005 |
Radiation | Monochromator: GLOEBEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 52428 / Num. obs: 47220 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.31 % / Rsym value: 0.0341 / Net I/σ(I): 25.15 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 2.11 % / Mean I/σ(I) obs: 3.82 / Num. unique all: 1972 / Rsym value: 0.2589 / % possible all: 56.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FW0 Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.094 / ESU R Free: 0.092 / 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: 13.533 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1874 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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