Primary Citation PubMed: 22992047 Citations in PubMed
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The substrate/product-binding modes of a novel GH120 ?-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485.
(2012) Biochem J 448
PubMed: 22992047 | PubMedCentral: PMC3507262 | DOI: 10.1042/BJ20121359
The atomic co-ordinates and structural factors for the wild-type Thermoanaerobacterium saccharolyticum JW/SL-YS485 XylC in complex with Tris (code 3VST), xylobiose (code 3VSU) and xylose (code 3VSV) h... ve been deposited in the RCSB PDB.
Parameter XylC–Tris (PDB code 3VST) XylC–xylobiose (PDB code 3VSU) XylC–xylose (PDB code 3VSV) Data collection Wavelength (Å) 1.00 1.00 1.00 Resolution (Å) 25–1.75 (1.81–1.75) 25–2.05 (2.12–2.05) 25–1.48 (1.53–1.48) Space group P 2 1 Unit cell a / b / c (Å) 88.64/202.24/99.92 88.68/202.31/100.40 88.78/201.95/100.11 β ( o ) 99.186 99.141 99.177 Number of reflections Measured 1471142 (145181) 902385 (68612) 2097975 (200889) Unique 346368 (34567) 212277 (19059) 574432 (57397) Completeness (%) 99.8 (99.9) 98.2 (88.4) 100.0 (100.0) R merge (%) 6.2 (37.5) 14.0 (49.0) 7.1 (49.6) Mean I /σ( I ) 19.1 (2.5) 8.5 (1.6) 20.9 (3.3) Multiplicity 4.2 (4.2) 4.3 (3.6) 3.7 (3.5) Refinement Number of reflections used 332107 (30562) 197345 (14891) 548128 (49577) R work (%) 15.1 (21.6) 15.3 (24.0) 15.0 (21.7) R f ree (%) 17.6 (23.7) 19.4 (27.6) 16.8 (22.8) Geometry deviations Bond lengths (Å) 0.015 0.015 0.015 Bond angles ( o ) 1.77 1.78 1.74 Number of atoms/mean B -values (Å 2 ) Protein atoms 20588/16.6 20588/17.3 20588/13.7 Tris atoms 32/13.6 – – Xylose atoms – – 350/34.1 Xylobiose atoms – 76/38.3 – Water molecules 3164/32.9 2518/32.8 3614/34.0 Ramachandran plot (%) Most favoured 86.9 86.2 87.4 Additionally allowed 12.7 13.4 12.3 Disallowed 0.4 0.4 0.4 Mutant production and specific activity measurement Site-directed mutagenesis was performed by inverse PCR and circulation of PCR products using the wild-type xylosidase gene in the expression plasmid pHsh- xylC [ 4 ].
Publication Year: 2012
