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Yorodumi- PDB-7zoo: Carbohydrate binding domain CBMXX from a multi-catalytic glucanas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zoo | |||||||||
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Title | Carbohydrate binding domain CBMXX from a multi-catalytic glucanase-chitinase from Chitinophaga pinensis DSM 2588 in complex with gentiobiose | |||||||||
Components | Carbohydrate binding domain XX | |||||||||
Keywords | CARBOHYDRATE / beta-trefoil / carbohydrate binding domain / beta-glycan | |||||||||
Function / homology | beta-D-glucopyranose Function and homology information | |||||||||
Biological species | Chitinophaga pinensis DSM 2588 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | |||||||||
Authors | Mazurkewich, S. / McKee, L.S. / Lu, Z. / Branden, G. / Larsbrink, J. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: To Be Published Title: CBMXX: A new family of Carbohydrate Binding Modules displaying three distinct ligand binding sites with affinity for beta-glucans. Authors: Mazurkewich, S. / McKee, L.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zoo.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zoo.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/7zoo ftp://data.pdbj.org/pub/pdb/validation_reports/zo/7zoo | HTTPS FTP |
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-Related structure data
Related structure data | 7zohSC 7zoiC 7zonC 7zopC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16176.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chitinophaga pinensis DSM 2588 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) #2: Sugar | #3: Water | ChemComp-HOH / | 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: 2.68 Å3/Da / Density % sol: 54.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M citrate buffer pH 5.5 with 12.5 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.991873 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.991873 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→29.56 Å / Num. obs: 27998 / % possible obs: 95.66 % / Redundancy: 6.6 % / Biso Wilson estimate: 35.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.25 |
Reflection shell | Resolution: 1.84→1.91 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 2117 / CC1/2: 0.947 / % possible all: 72.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZOH Resolution: 1.84→29.56 Å / SU ML: 0.2278 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.5478 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→29.56 Å
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Refine LS restraints |
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LS refinement shell |
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