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Yorodumi- PDB-2cdo: structure of agarase carbohydrate binding module in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cdo | |||||||||
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Title | structure of agarase carbohydrate binding module in complex with neoagarohexaose | |||||||||
Components | BETA-AGARASE 1 | |||||||||
Keywords | HYDROLASE / CARBOHYDRATE-BINDING MODULE | |||||||||
Function / homology | Function and homology information beta-agarase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | SACCHAROPHAGUS DEGRADANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å | |||||||||
Authors | Henshaw, J. / Horne, A. / Van Bueren, A.L. / Money, V.A. / Bolam, D.N. / Czjzek, M. / Weiner, R.M. / Hutcheson, S.W. / Davies, G.J. / Boraston, A.B. / Gilbert, H.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Family 6 Carbohydrate Binding Modules in Beta-Agarases Display Exquisite Selectivity for the Non- Reducing Termini of Agarose Chains. Authors: Henshaw, J. / Horne, A. / Van Bueren, A.L. / Money, V.A. / Bolam, D.N. / Czjzek, M. / Ekborg, N.A. / Weiner, R.M. / Hutcheson, S.W. / Davies, G.J. / Boraston, A.B. / Gilbert, H.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdo.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdo.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cdo_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2cdo_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2cdo_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 2cdo_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdo ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 17105.768 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 456-593 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DN99 #2: Polysaccharide | 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L- ...3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 624 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 460 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 532 TO MET ...ENGINEERED |
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Sequence details | RESIDUE 23 (NUMBERED 1 IN THE PDB FILE) IN THE GIVEN SEQUENCE CORRESPONDS TO RESIDUE 456 IN THE ...RESIDUE 23 (NUMBERED 1 IN THE PDB FILE) IN THE GIVEN SEQUENCE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51 % |
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Crystal grow | pH: 7.5 Details: 2 M NACL, 16-20 % PEG 4000, BUFFERED TO PH 7.5 WITH 100 MM TRIS/HCL. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97910,0.97565,0.97950 | ||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: May 8, 2005 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: SILICON (1 1 1) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→96.12 Å / Num. obs: 35218 / % possible obs: 69.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.9 | ||||||||||||
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.7 / % possible all: 11.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.64→98.53 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 1.99 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→98.53 Å
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Refine LS restraints |
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