2XJR

X-ray structure of the N-terminal domain of the flocculin Flo5 from Saccharomyces cerevisiae in complex with calcium and Man5(D2-D3)

• PDB DOI: https://doi.org/10.2210/pdb2XJR/pdb

• Classification: CELL ADHESION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-06 Released: 2010-12-15 
• Deposition Author(s): Veelders, M., Brueckner, S., Ott, D., Unverzagt, C., Moesch, H.-U., Essen, L.-O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.140 
• R-Value Work: 0.113 
• R-Value Observed: 0.114 

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: 28.65 kDa 
• Atom Count: 2,665 
• Modelled Residue Count: 257 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLOCCULATION PROTEIN FLO5	A	258	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38894 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38894  Go to UniProtKB:  P38894

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G84430BE GlyCosmos:  G84430BE GlyGen:  G84430BE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.140 
• R-Value Work: 0.113 
• R-Value Observed: 0.114 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.46	α = 90
b = 61.91	β = 90
c = 106.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Veelders, M., Brueckner, S., Ott, D., Unverzagt, C., Moesch, H.-U., Essen, L.-O.

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary