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Yorodumi- PDB-4d6j: Crystal structure of a family 98 glycoside hydrolase catalytic mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d6j | |||||||||
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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 X01 mutant) | |||||||||
Components | GLYCOSIDE HYDROLASE | |||||||||
Keywords | HYDROLASE / BLOOD GROUP ANTIGEN | |||||||||
Function / homology | Function and homology information family 98 glycoside hydrolase / arginine biosynthesis bifunctional protein fold / Polysaccharide lyase family 8-like, C-terminal / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | |||||||||
Authors | Kwan, D.H. / Constantinescu, I. / Chapanian, R. / Higgins, M.A. / Samain, E. / Boraston, A.B. / Kizhakkedathu, J.N. / Withers, S.G. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d6j.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d6j.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 4d6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d6j_validation.pdf.gz | 891.2 KB | Display | wwPDB validaton report |
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Full document | 4d6j_full_validation.pdf.gz | 897.1 KB | Display | |
Data in XML | 4d6j_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 4d6j_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/4d6j ftp://data.pdbj.org/pub/pdb/validation_reports/d6/4d6j | HTTPS FTP |
-Related structure data
Related structure data | 4d6cC 4d6dC 4d6eC 4d6fC 4d6gC 4d6hC 4d6iC 4d71C 4d72C 2wmiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 69047.617 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.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: SP3-BS71 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5LBQ0, 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 | #4: Water | ChemComp-HOH / | Nonpolymer details | BETA-D-GALACTOSE (GAL): PART OF THE BLOOD GROUP A-TETRASACCHARIDE SUBSTRATE ALPHA-L-FUCOSE (FUC): ...BETA-D-GALACTOSE (GAL): PART OF THE BLOOD GROUP A-TETRASACCH | Sequence details | CATALYTIC MODULE (RESIDUES 421-1006) | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.06 % / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 |
Detector | Type: RIGAKU R-AXIS 4 / 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: 1.98→30.65 Å / Num. obs: 48464 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WMI Resolution: 1.98→30.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.183 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.148 / 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: 13.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→30.65 Å
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Refine LS restraints |
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