6RS7

X-ray crystal structure of LsAA9B (deglycosylated form)

• PDB DOI: https://doi.org/10.2210/pdb6RS7/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Panus similis
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2019-05-21 Released: 2019-09-11 
• Deposition Author(s): Frandsen, K.E.H., Tovborg, M., Poulsen, J.C.N., Johansen, K.S., Lo Leggio, L.
• Funding Organization(s): Danish Agency for Science Technology and Innovation, Novo Nordisk Foundation, European Communitys Seventh Framework Programme, European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.211 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 

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: 24.76 kDa 
• Atom Count: 2,028 
• Modelled Residue Count: 221 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AA9	A	221	Panus similis	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	C [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
PGE	M [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NO3	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.211 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.08	α = 90
b = 72.99	β = 90
c = 79.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Frandsen, K.E.H., Tovborg, M., Poulsen, J.C.N., Johansen, K.S., Lo Leggio, L.

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Funding Organization	Location	Grant Number
Danish Agency for Science Technology and Innovation	Denmark	12-134922
Danish Agency for Science Technology and Innovation	Denmark	12-134923
Novo Nordisk Foundation	Denmark	NNF17SA0027704
European Communitys Seventh Framework Programme	Denmark	BioStruct-X (grant agreement N283570)
European Commission	Denmark	CF16-0673 - The Carlsberg Foundation
European Commission	Denmark	CF17-0533 - The Carlsberg Foundation
European Commission	France	AgreenSkills+ (Marie-Curie FP7 COFUND People Programme under grant agreement 609398)

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2021-11-10
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 3.1: 2024-01-24
  Changes: Data collection, Refinement description