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- PDB-4d71: Crystal structure of a family 98 glycoside hydrolase catalytic mo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d71 | ||||||||||||
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Title | Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 2 blood group A-tetrasaccharide (E558A X02 mutant) | ||||||||||||
![]() | GLYCOSIDE HYDROLASE | ||||||||||||
![]() | HYDROLASE / BLOOD GROUP ANTIGEN | ||||||||||||
Function / homology | ![]() blood-group-substance endo-1,4-beta-galactosidase / blood-group-substance endo-1,4-beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Kwan, D.H. / Constantinescu, I. / Chapanian, R. / Higgins, M.A. / Samain, E. / Boraston, A.B. / Kizhakkedathu, J.N. / Withers, S.G. | ||||||||||||
![]() | ![]() Title: Towards Efficient Enzymes for the Generation of Universal Blood Through Structure-Guided Directed Evolution. Authors: Kwan, D.H. / Constantinescu, I. / Chapanian, R. / Higgins, M.A. / Koetzler, M. / Samain, E. / Boraston, A.B. / Kizhakkedathu, J.N. / Withers, S.G. | ||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.8 KB | Display | ![]() |
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PDB format | ![]() | 118.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 892.5 KB | Display | ![]() |
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Full document | ![]() | 898.6 KB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 48.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d6cC ![]() 4d6dC ![]() 4d6eC ![]() 4d6fC ![]() 4d6gC ![]() 4d6hC ![]() 4d6iC ![]() 4d6jC ![]() 4d72C ![]() 2wmiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 68706.180 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 423-1005 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5LBQ0, UniProt: A0A0H2UKY3*PLUS, blood-group-substance endo-1,4-beta-galactosidase | ||||
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Nonpolymer details | BETA-D-GALACTOSE (GAL): PART OF THE A-TETRASACCHARIDE SUBSTRATE ALPHA-L-FUCOSE (FUC): PART OF THE A- ...BETA-D-GALACTOSE (GAL): PART OF THE A-TETRASACCH | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.47 % / Description: NONE |
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Crystal grow | Details: 15% PEG 3350, 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU R-AXIS 4 / Detector: IMAGE PLATE / Details: OSMIC BLUE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→30.73 Å / Num. obs: 68082 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.2 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WMI Resolution: 1.77→30.31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.991 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.108 / 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: 15.457 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→30.31 Å
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Refine LS restraints |
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