5XC2 | pdb_00005xc2

Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminarihexaose

• PDB DOI: https://doi.org/10.2210/pdb5XC2/pdb

• Classification: HYDROLASE
• Organism(s): Rhizomucor miehei
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-03-22 Released: 2018-03-28 
• Deposition Author(s): Qin, Z., Yang, S., Peng, Z., Yan, Q., Jiang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Catalytic mechanism of glycoside hydrolase family 81 beta-1,3-glucanase

Yang, S., Qin, Z., Zhou, P., Yan, Q., Jiang, Z.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 367.03 kDa 
• Atom Count: 23,075 
• Modeled Residue Count: 2,790 
• Deposited Residue Count: 3,184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-beta-1,3-glucanase	A, B, C, D	796	Rhizomucor miehei	Mutation(s): 0  EC: 3.2.1.39
UniProt
Find proteins for A0A023I7E1 (Rhizomucor miehei) Explore A0A023I7E1  Go to UniProtKB:  A0A023I7E1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	E	6		N/A
Glycosylation Resources
GlyTouCan:  G41202OE GlyCosmos:  G41202OE GlyGen:  G41202OE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	F, M	5		N/A
Glycosylation Resources
GlyTouCan:  G03330ED GlyCosmos:  G03330ED

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	G, L, O, P, Q	4		N/A
Glycosylation Resources
GlyTouCan:  G87841AX GlyCosmos:  G87841AX GlyGen:  G87841AX

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	H, I, N, R	3		N/A
Glycosylation Resources
GlyTouCan:  G00024MO GlyCosmos:  G00024MO GlyGen:  G00024MO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	J, K	2		N/A
Glycosylation Resources
GlyTouCan:  G36535HU GlyCosmos:  G36535HU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024	J, K	beta-laminaribiose	Oligosaccharide / Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.7	α = 90
b = 99.02	β = 111.35
c = 138.43	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: 2018-03-28 
Deposition Author(s): Qin, Z., Yang, S., Peng, Z., Yan, Q., Jiang, Z.

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2023-11-22
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary