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Yorodumi- PDB-4jso: The X-ray crystal structure of a thermophilic cellobiose binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jso | |||||||||
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Title | The X-ray crystal structure of a thermophilic cellobiose binding protein bound with laminaripentaose | |||||||||
Components | Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / THERMOPHILIC PROTEIN / CELLULOSE / CELLOPENTAOSE / LAMINARIBIOSE / LAMINARPENTAOSE BINDING PROTEIN | |||||||||
Function / homology | Function and homology information peptide transport / peptide transmembrane transporter activity / outer membrane-bounded periplasmic space Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | |||||||||
Authors | Munshi, P. / Cuneo, M.J. | |||||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2013 Title: Molecular details of ligand selectivity determinants in a promiscuous beta-glucan periplasmic binding protein. Authors: Munshi, P. / Stanley, C.B. / Ghimire-Rijal, S. / Lu, X. / Myles, D.A. / Cuneo, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jso.cif.gz | 140 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jso.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/4jso ftp://data.pdbj.org/pub/pdb/validation_reports/js/4jso | HTTPS FTP |
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-Related structure data
Related structure data | 4jsdSC 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: 67410.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM0031, TM_0031 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: Q9WXN8 |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.05 Å3/Da / Density % sol: 40.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: tmCBP was concentrated to 20 mg/mL and dialyzed into 10 mM Tris, 40 mM NaCl, 0.5 mM TCEP for crystallization. Laminaripentaose was added to a final concentration of 1 mM prior to ...Details: tmCBP was concentrated to 20 mg/mL and dialyzed into 10 mM Tris, 40 mM NaCl, 0.5 mM TCEP for crystallization. Laminaripentaose was added to a final concentration of 1 mM prior to crystallization trials. Crystals were grown in drops containing 2 uL of the protein solution mixed with 2 uL of 0.2-0.3 M magnesium acetate or calcium acetate, 20-30% (wt/vol) PEG 3350 equilibrated against 900 uL of the same solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. all: 33022 / Num. obs: 32940 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.037 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.07→2.13 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2783 / Rsym value: 0.368 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JSD Resolution: 2.07→48.075 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 24.59 / 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: 2.07→48.075 Å
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Refine LS restraints |
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LS refinement shell |
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