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Yorodumi- PDB-6lzt: N409A mutant of chitin-specific solute binding protein from Vibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lzt | |||||||||
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Title | N409A mutant of chitin-specific solute binding protein from Vibrio harveyi co-crystalized 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: 1.853 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 | 6lzt.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lzt.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 6lzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/6lzt ftp://data.pdbj.org/pub/pdb/validation_reports/lz/6lzt | HTTPS FTP |
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-Related structure data
Related structure data | 6lzqC 6lzuC 6lzvC 6lzwC 7ebiC 7ebmC 5yqwS S: Starting model for refinement C: citing same article (ref.) |
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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: 61002.758 Da / Num. of mol.: 1 / Mutation: N409A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio harveyi (strain 1DA3) (bacteria) 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 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.5 Details: 1.63mM chitobiose, 0.06 M Divalents (MgCl2, CaCl2), 0.1M Buffer System 1 (Imidazole, MES (acid)), pH 6.5, 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: 0.99984 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 6, 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: 1.85→50 Å / Num. obs: 44321 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.067 / Rrim(I) all: 0.131 / Rsym value: 0.131 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 0.687 / Num. unique obs: 2194 / CC1/2: 0.817 / Rpim(I) all: 0.423 / Rrim(I) all: 0.809 / Rsym value: 1.393 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5yqw Resolution: 1.853→23.647 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.853→23.647 Å
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Refine LS restraints |
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LS refinement shell |
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