5UPM | pdb_00005upm

Crystal structure of BhGH81 mutant in complex with laminaro-triose

• PDB DOI: https://doi.org/10.2210/pdb5UPM/pdb

• Classification: HYDROLASE
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-02-03 Released: 2017-06-28 
• Deposition Author(s): Pluvinage, B., Boraston, A.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.146 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

The quaternary structure of beta-1,3-glucan contributes to its recognition and hydrolysis by a multimodular family 81 glycoside hydrolase

Pluvinage, B., Fillo, A., Massel, P., Boraston, A.B.

(2017) Structure 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.17 kDa 
• Atom Count: 7,249 
• Modeled Residue Count: 753 
• Deposited Residue Count: 753 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH0236 protein	A	753	Halalkalibacterium halodurans C-125	Mutation(s): 1  Gene Names: BH0236 EC: 3.2.1.39
UniProt
Find proteins for Q9KG76 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KG76  Go to UniProtKB:  Q9KG76

Oligosaccharides

Help  

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan: G51422BS GlyCosmos: G51422BS GlyGen: G51422BS

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan: G36535HU GlyCosmos: G36535HU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024	D	beta-laminaribiose	Oligosaccharide / Antimicrobial

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.146 (Depositor) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.52	α = 90
b = 93.68	β = 90
c = 159.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Pluvinage, B., Boraston, A.B.

Revision History  

• Version 1.0: 2017-06-28
  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: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary