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Yorodumi- PDB-2zyk: Crystal structure of cyclo/maltodextrin-binding protein complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zyk | ||||||||||||
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Title | Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin | ||||||||||||
Components | Solute-binding protein | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / solute-binding protein / closed form | ||||||||||||
Function / homology | Function and homology information carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing Similarity search - Function | ||||||||||||
Biological species | Thermoactinomyces vulgaris (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||
Authors | Tonozuka, T. / Sogawa, A. / Yamada, M. / Matsumoto, N. / Yoshida, H. / Kamitori, S. / Ichikawa, K. / Mizuno, M. / Nishikawa, A. / Sakano, Y. | ||||||||||||
Citation | Journal: Febs J. / Year: 2007 Title: Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein Authors: Tonozuka, T. / Sogawa, A. / Yamada, M. / Matsumoto, N. / Yoshida, H. / Kamitori, S. / Ichikawa, K. / Mizuno, M. / Nishikawa, A. / Sakano, Y. #1: Journal: Febs J. / Year: 2009 Title: Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein Authors: Matsumoto, M. / Yamada, M. / Kurakata, Y. / Yoshida, H. / Kamitori, S. / Nishikawa, A. / Tonozuka, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zyk.cif.gz | 313.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zyk.ent.gz | 259.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zyk_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 2zyk_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 2zyk_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 2zyk_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/2zyk ftp://data.pdbj.org/pub/pdb/validation_reports/zy/2zyk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 43686.863 Da / Num. of mol.: 4 / Fragment: residues 1-397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Strain: R-47 / Plasmid: pETCBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJF5 #2: Polysaccharide | Cyclooctakis-(1-4)-(alpha-D-glucopyranose) / gamma-cyclodextrin #3: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 38.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 25% PEG 6000, 0.1M MES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 47691 / Num. obs: 47691 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.5→2.66 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 8.6 / Num. unique all: 4735 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: a rough model of the selenomethionine-substituted protein Resolution: 2.5→48.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3030046.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.0713 Å2 / ksol: 0.361716 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→48.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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