5XBZ | pdb_00005xbz

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

• PDB DOI: https://doi.org/10.2210/pdb5XBZ/pdb

• Classification: HYDROLASE
• Organism(s): Rhizomucor miehei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-21 Released: 2018-03-28 
• Deposition Author(s): Yang, S., Qin, Z., Zhou, P., Yan, Q., Jiang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.190 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.174 (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.

Macromolecule Content 

• Total Structure Weight: 183.5 kDa 
• Atom Count: 11,705 
• Modeled Residue Count: 1,415 
• Deposited Residue Count: 1,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-beta-1,3-glucanase	A, B	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	C, F, G	5		N/A
Glycosylation Resources
GlyTouCan:  G03330ED GlyCosmos:  G03330ED

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	D, H	4		N/A
Glycosylation Resources
GlyTouCan:  G87841AX GlyCosmos:  G87841AX GlyGen:  G87841AX

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	E	3		N/A
Glycosylation Resources
GlyTouCan:  G00024MO GlyCosmos:  G00024MO GlyGen:  G00024MO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.190 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.916	α = 90
b = 96.958	β = 93.91
c = 127.642	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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): Yang, S., Qin, Z., Zhou, P., 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: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary