5YLK

Complex structure of GH 113 family beta-1,4-mannanase with mannobiose

• PDB DOI: https://doi.org/10.2210/pdb5YLK/pdb

• Classification: HYDROLASE
• Organism(s): Amphibacillus xylanus NBRC 15112
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-17 Released: 2018-06-20 
• Deposition Author(s): Jiang, Z.Q., You, X., Yang, S.Q., Huang, P., Ma, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.195 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74 kDa 
• Atom Count: 5,683 
• Modelled Residue Count: 618 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-1,4-mannanase	A [auth B], B [auth A]	309	Amphibacillus xylanus NBRC 15112	Mutation(s): 1  Gene Names: AXY_22370
UniProt
Find proteins for K0J0N5 (Amphibacillus xylanus (strain ATCC 51415 / DSM 6626 / JCM 7361 / LMG 17667 / NBRC 15112 / Ep01)) Explore K0J0N5  Go to UniProtKB:  K0J0N5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	C, D, E, F	2		N/A
Glycosylation Resources
GlyTouCan:  G78317QO GlyCosmos:  G78317QO GlyGen:  G78317QO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	G [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900115	C, D, E, F	4beta-beta-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.195 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.985	α = 90
b = 72.177	β = 90
c = 177.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Jiang, Z.Q., You, X., Yang, S.Q., Huang, P., Ma, J.W.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2018-08-08
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary