+Open data
-Basic information
Entry | Database: PDB / ID: 8c8f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the E. coli maltodextrin-binding protein | ||||||
Components | Maltose/maltodextrin-binding periplasmic protein | ||||||
Keywords | SUGAR BINDING PROTEIN / Maltose Binding Protein / Native MBP | ||||||
Function / homology | Maltose/Cyclodextrin ABC transporter, substrate-binding protein / carbohydrate transmembrane transporter activity / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / outer membrane-bounded periplasmic space / DI(HYDROXYETHYL)ETHER / Maltose/maltodextrin-binding periplasmic protein Function and homology information | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Marquez Espinoza, A. / Rodrigues, M.J. / Olieric, V. / Freisinger, E. | ||||||
Funding support | Switzerland, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of the E. coli maltodextrin-binding protein Authors: Marquez Espinoza, A. / Rodrigues, M.J. / Olieric, V. / Freisinger, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8c8f.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8c8f.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 8c8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/8c8f ftp://data.pdbj.org/pub/pdb/validation_reports/c8/8c8f | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43436.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria) / References: UniProt: P0AEY0 |
---|---|
#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.99 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 7.4, 30 % PEG Smear Broad, 0.1 M NaBr and 0.1 M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→56.04 Å / Num. obs: 110383 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.15→1.17 Å / Num. unique obs: 5258 / CC1/2: 0.799 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→37.76 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.965 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 10.422 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.15→37.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|