4IIS

Crystal structure of a glycosylated beta-1,3-glucanase (HEV B 2), An allergen from Hevea Brasiliensis (Space group P41)

• PDB DOI: https://doi.org/10.2210/pdb4IIS/pdb
• Entry: 4IIS supersedes: 3F55

• Classification: HYDROLASE
• Organism(s): Hevea brasiliensis
• Mutation(s): No 


• Deposited: 2012-12-20 Released: 2013-11-27 
• Deposition Author(s): Rodriguez-Romero, A., Hernandez-Santoyo, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.220 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

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: 142.43 kDa 
• Atom Count: 10,016 
• Modelled Residue Count: 1,264 
• Deposited Residue Count: 1,264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-1,3-glucanase form 'RRII Gln 2'	A, B, C, D	316	Hevea brasiliensis	Mutation(s): 0  EC: 3.2.1.39
UniProt
Find proteins for D1M8S7 (Hevea brasiliensis) Explore D1M8S7  Go to UniProtKB:  D1M8S7

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	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	F [auth A], G [auth A], J [auth D]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
CAC	H [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
NA	I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B, C, D	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.220 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.118	α = 90
b = 150.118	β = 90
c = 77.331	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Rodriguez-Romero, A., Hernandez-Santoyo, A.
• This entry supersedes: 3F55

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-03-19
  Changes: Database references
• Version 2.0: 2019-12-25
  Changes: Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary