3VZK: Endo-1,4-beta-xylanase

Name: PDB 3VZK: Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant
Published: 2013-05-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant. Determined by X-ray diffraction at 1.55 Å resolution. Released 8 May 2013.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Bacillus circulans
Chains: 2
Atoms: 3,384
Mol. weight: 41.04 kDa
Released: 8 May 2013

Explore 3VZK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VZK contains 6 α-helices and 26 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
β-strand	15-20	6	2
β-strand	25-31	7	2
β-strand	35-42	8	1
β-strand	50-61	12	2
β-strand	64-73	10	1
β-strand	77-85	9	1
β-strand	93-100	8	1
β-strand	103-117	15	1
β-strand	120-132	13	1
α-helix	135-137	3
β-strand	142-145	4	2
α-helix	146-155	10
β-strand	163-174	12	1
β-strand	177-184	8	2

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	3
β-strand	15-20	6	4
β-strand	25-31	7	4
β-strand	35-42	8	3
α-helix	49	1
β-strand	50-61	12	4
β-strand	64-73	10	3
β-strand	77-85	9	3
β-strand	93-100	8	3
β-strand	103-112	10	3
β-strand	125-132	8	3
α-helix	135-137	3
β-strand	142-145	4	4
α-helix	146-155	10
α-helix	159-161	3
β-strand	163-174	12	3
β-strand	177-184	8	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endo-1,4-beta-xylanase	A, B	protein	185	Bacillus circulans	P09850 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3VZK_1 Endo-1,4-beta-xylanase (chains A, B)
ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGEFVVGKGWTTGSPFRTINYNAGVWAP
NGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDG
DRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSS
NVTVW

Primary citation

Strategies for modulating the pH-dependent activity of a family 11 glycoside hydrolase. Ludwiczek, M.L., D'Angelo, I., Yalloway, G.N. et al. Biochemistry (2013) 52:3138-3156. DOI 10.1021/bi400034m · PubMed

Other PDB entries of the same protein (UniProt P09850 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QY3 1.24 Å, Xylanase from Bacillus circulans mutant E78Q/F125A bound to xylotriose
8R85 1.3 Å, Xylanase from Bacillus circulans mutant E78Q/W9A
8QXY 1.41 Å, Xylanase from Bacillus circulans mutant E78Q bound to xylotriose
1XNB 1.49 Å, High-resolution structures of xylanases from B. Circulans and T. Harzianum identify a…
2BVV 1.5 Å, Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
8QXZ 1.5 Å, Xylanase from Bacillus circulans mutant E78Q/Y69A
8R86 1.5 Å, Xylanase from Bacillus circulans mutant E78Q/W71A
1C5H 1.55 Å, Hydrogen bonding and catalysis: an unexpected explanation for how a single amino acid…
1HV0 1.6 Å, Dissecting electrostatic interactions and the PH-dependent activity of a family 11…
1XNC 1.6 Å, Thermostabilization of the bacillus circulans xylanase, by the introduction of disulfide…
3VZN 1.67 Å, Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant…
8QY2 1.7 Å, Xylanase from Bacillus circulans mutant E78Q/F125A

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