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Yorodumi- PDB-1of3: Structural and thermodynamic dissection of specific mannan recogn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1of3 | ||||||
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Title | Structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, TmCBM27 | ||||||
Components | BETA-MANNOSIDASE | ||||||
Keywords | HYDROLASE/CARBOHYDRATE BINDING / MANNAN BINDING / CARBOHYDRATE BINDING MODULE / POLYSACCHARIDE DEGRADATION / TMCBM27 / HYDROLASE / HYDROLASE-CARBOHYDRATE BINDING complex | ||||||
Function / homology | Function and homology information mannan endo-1,4-beta-mannosidase activity / metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Boraston, A.B. / Revett, T.J. / Boraston, C.M. / Nurizzo, D. / Davies, G.J. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structural and Thermodynamic Dissection of Specific Mannan Recognition by a Carbohydrate Binding Module, Tmcbm27 Authors: Boraston, A.B. / Revett, T.J. / Boraston, C.M. / Nurizzo, D. / Davies, G.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1of3.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1of3.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 1of3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1of3_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 1of3_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 1of3_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 1of3_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1of3 ftp://data.pdbj.org/pub/pdb/validation_reports/of/1of3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20629.701 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 505-680 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Plasmid: PET 28-TMCBM27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RIK9 #2: Chemical | #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: 3.32 Å3/Da / Density % sol: 62.92 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 1.6 M NA K PHOSPHATE, 0.1 M NA HEPES PH 7.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9202 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 36721 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 8.1 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 100 % / Redundancy: 8 % |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.908 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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