› 4s2d

Hybrid

Joint X-ray/neutron structure of Trichoderma reesei xylanase II in complex with MES at pH 5.7

Released:
DOI: 10.2210/pdb4s2d/pdb
PDB entry 4s2d coloured by chain, front view.
PDB entry 4s2d coloured by chain, side view.
PDB entry 4s2d coloured by chain, top view.
Source organism: Trichoderma reesei
Primary publication:
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
Wan Q, Parks JM, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L, Langan P, Kovalevsky A
Proc Natl Acad Sci U S A 112 12384-9 (2015)
PMID: 26392527

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153153 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endo-1,4-beta-xylanase 2 Chain: A
Molecule details ›
Chain: A
Length: 190 amino acids
Theoretical weight: 20.84 KDa
Source organism: Trichoderma reesei
UniProt:
  • Canonical: P36217 (Residues: 34-223; Coverage: 93%)
Gene names: M419DRAFT_124931, xyn2
Sequence domains: Glycosyl hydrolases family 11
Structure domains: Jelly Rolls

Ligands and Environments

3 bound ligands:
Ligand IOD 1 x IOD
Ligand MES 1 x MES
Ligand DOD 151 x DOD
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Experimental Method: Neutron Diffraction, X-ray diffraction
X-ray source: RIGAKU MICROMAX-007 HF, OTHER
Spacegroup: P212121
Unit cell:
a: 49.174Å b: 60.214Å c: 70.434Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.192 0.196

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Citations

1 review citation

The use of neutron scattering to determine the functional structure of glycoside hydrolase.
Nakamura et al. (2016)
15 other articles

3 mentions without citation

Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography.
Chen et al. (2017)
2 more