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Yorodumi- PDB-4b3k: Family 1 6-phospho-beta-D glycosidase from Streptococcus pyogenes -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b3k | ||||||
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Title | Family 1 6-phospho-beta-D glycosidase from Streptococcus pyogenes | ||||||
Components | BETA-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / CARBOHYDRATE-ACTIVE ENZYME | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PYOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Stepper, J. / Dabin, J. / Ekloef, J.M. / Thongpoo, P. / Kongsaeree, P.T. / Taylor, E.J. / Turkenburg, J.P. / Brumer, H. / Davies, G.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure and Activity of the Streptococcus Pyogenes Family Gh1 6-Phospho Beta-Glycosidase Spy1599 Authors: Stepper, J. / Dabin, J. / Ekloef, J.M. / Thongpoo, P. / Kongsaeree, P.T. / Taylor, E.J. / Turkenburg, J.P. / Brumer, H. / Davies, G.J. | ||||||
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. THE SHEETS PRESENTED AS "CA" 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. THE SHEETS PRESENTED AS "DA" 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. THE SHEETS PRESENTED AS "EA" 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. THE SHEETS PRESENTED AS "FA" 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 | 4b3k.cif.gz | 544.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b3k.ent.gz | 451.8 KB | Display | PDB format |
PDBx/mmJSON format | 4b3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b3k_validation.pdf.gz | 474.1 KB | Display | wwPDB validaton report |
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Full document | 4b3k_full_validation.pdf.gz | 543.3 KB | Display | |
Data in XML | 4b3k_validation.xml.gz | 97.3 KB | Display | |
Data in CIF | 4b3k_validation.cif.gz | 129.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b3k ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b3k | HTTPS FTP |
-Related structure data
Related structure data | 4b3lC 1od0S 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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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 55040.555 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 GAS, SF370 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q99YP9, beta-glucosidase, 6-phospho-beta-glucosidase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS TRIS PROPANE PH7.5, 20% PEG 3350, 0.2M NAF |
-Data collection
Diffraction | Mean temperature: 120 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 | |||||||||||||||
Detector | Date: Sep 25, 2010 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.6→66.56 Å / Num. obs: 105767 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OD0 Resolution: 2.6→66.56 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.842 / SU B: 13.347 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.916 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.403 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→66.56 Å
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Refine LS restraints |
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