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Open data
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Basic information
Entry | Database: PDB / ID: 2cdp | |||||||||
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Title | Structure of a CBM6 in complex with neoagarohexaose | |||||||||
![]() | BETA-AGARASE 1 | |||||||||
![]() | HYDROLASE / CARBOHYDRATE-BINDING MODULE | |||||||||
Function / homology | ![]() beta-agarase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.7 KB | Display | ![]() |
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PDB format | ![]() | 106.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cdoSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 16882.111 Da / Num. of mol.: 4 / Fragment: CARBOHYDRATE-BINDING MODULE, RESIDUES 456-593 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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, 595 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
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 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
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Crystal grow | pH: 7.5 Details: 2M NACL, 16-20% PEG 4000 BUFFERED TO PH 7.5 WITH TRIS/HCL |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS-4 / Detector: IMAGE PLATE / Details: MULTIWIRE OPTICS |
Radiation | Monochromator: MULTIWIRE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→19.62 Å / Num. obs: 79215 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.1 |
Reflection shell | Redundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.9 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CDO Resolution: 1.59→19.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.272 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 18 TO 25 OF CHAINS B AND C AND RESIDUES 20 TO 25 OF CHAIN D ARE DISORDERED RESIDUES 19 AND 26 OF CHAIN D HAVE BEEN MODELLED WITH HALF OCCUPANCY
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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: 21.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→19.62 Å
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Refine LS restraints |
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