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Yorodumi- PDB-7ebi: Chitin-specific solute binding protein from Vibrio harveyi co-cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ebi | |||||||||
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Title | Chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitotetraose. | |||||||||
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: 1.5 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 | 7ebi.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ebi.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ebi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebi ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebi | HTTPS FTP |
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-Related structure data
Related structure data | 6lzqC 6lztC 6lzuC 6lzvC 6lzwC 7ebmC 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: 61288.059 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 |
-Non-polymers , 5 types, 329 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-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: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: 1.63mM chitotetramer, 0.06M Divalents (MgCl2, CaCl2), 0.1M Buffer System 1 (Imidazole, MES (acid)), pH 6.5, 30% v/v Precipitant Mix 2 (Ethylene glycol, PEG 8000) |
-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: 0.99984 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 89117 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Net I/σ(I): 19.99 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.3 % / Num. unique obs: 4293 / CC1/2: 0.762 / Rpim(I) all: 0.312 / Rrim(I) all: 0.506 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5yqw Resolution: 1.5→24.49 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.81 / 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: 1.5→24.49 Å
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Refine LS restraints |
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LS refinement shell |
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