[English] 日本語
Yorodumi- PDB-4d6g: Crystal structure of a family 98 glycoside hydrolase catalytic mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d6g | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the blood group A-trisaccharide (L19 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4d6g.cif.gz | 309.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4d6g.ent.gz | 246.3 KB | Display | PDB format |
PDBx/mmJSON format | 4d6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d6g_validation.pdf.gz | 930.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4d6g_full_validation.pdf.gz | 938.9 KB | Display | |
Data in XML | 4d6g_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 4d6g_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/4d6g ftp://data.pdbj.org/pub/pdb/validation_reports/d6/4d6g | HTTPS FTP |
-Related structure data
Related structure data | 4d6cC 4d6dC 4d6eC 4d6fC 4d6hC 4d6iC 4d6jC 4d71C 4d72C 2wmiS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 69068.578 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, 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 |
---|---|
#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | BETA-D-GALACTOSE (GAL): PART OF THE A-TRISACCHARIDE PRODUCT. ALPHA-L-FUCOSE (FUC): PART OF THE A- ...BETA-D-GALACTOSE (GAL): PART OF THE A-TRISACCHAR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.71 % / Description: NONE |
---|---|
Crystal grow | Details: 15% PEG 3350, 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Type: CLSI / Wavelength: 0.98005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98005 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→48.13 Å / Num. obs: 192579 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.24→1.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.7 / % possible all: 98 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WMI Resolution: 1.24→48.33 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.849 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 9.731 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.24→48.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|