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Yorodumi- PDB-7ebm: W363A mutant of Chitin-specific solute binding protein from Vibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ebm | |||||||||
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Title | W363A mutant of Chitin-specific solute binding protein from Vibrio harveyi in complex with chitobiose. | |||||||||
Components | Peptide ABC transporter, periplasmic peptide-binding protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / complex / chitin / periplasmic solute-binding protein / Vibrios | |||||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | |||||||||
Biological species | Vibrio harveyi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Kitaoku, Y. / Ubonbal, P. / Tran, L.T. / Robinson, R.C. / Suginta, W. | |||||||||
Funding support | Thailand, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: A structural model for (GlcNAc) 2 translocation via a periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria. Authors: Kitaoku, Y. / Fukamizo, T. / Kumsaoad, S. / Ubonbal, P. / Robinson, R.C. / Suginta, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ebm.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ebm.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ebm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebm ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebm | HTTPS FTP |
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-Related structure data
Related structure data | 6lzqC 6lztC 6lzuC 6lzvC 6lzwC 7ebiC 5yqwS 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 61172.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (strain 1DA3) (bacteria) Strain: 1DA3 / Gene: VME_26970 / Production host: Escherichia coli (E. coli) / References: UniProt: D0XC84 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 266 molecules
#3: Chemical | ChemComp-EDO / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 1.63mM chitobiose, 0.06M Divalents (MgCl2, CaCl2), 0.1M Buffer System 2 (Sodium HEPES, MOPS (acid)), pH 7.5, 50% v/v Precipitant Mix 4 (MPD, PEG 1000, PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97913 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 40844 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rpim(I) all: 0.075 / Rrim(I) all: 0.199 / Net I/σ(I): 401.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 2018 / CC1/2: 0.572 / Rpim(I) all: 0.796 / Rrim(I) all: 2.03 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5yqw Resolution: 1.9→23.732 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→23.732 Å
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Refine LS restraints |
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LS refinement shell |
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