9GVB | pdb_00009gvb

Ruminococcus flavefaciens Coh-Doc complex between a group 2 Dockerin and the Cohesin from cell surface attached scaffoldin ScaE

• PDB DOI: https://doi.org/10.2210/pdb9GVB/pdb

• Classification: PROTEIN BINDING
• Organism(s): Ruminococcus flavefaciens FD-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-23 Released: 2025-10-08 
• Deposition Author(s): Bule, P., Carvalho, A.L., Najmudin, S.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Cohesin-Dockerin complexes from Ruminococcus flavefaciens with naturally truncated dockerins exhibit a triple-binding mode

Duarte, M., Carvalho, A.L., Romao, M.J., Prates, J.A.M., Najmudin, S., Bayer, E.A., Fontes, C.M.G.A., Bule, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.52 kDa 
• Atom Count: 2,181 
• Modeled Residue Count: 286 
• Deposited Residue Count: 347 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell-wall anchoring protein	A	203	Ruminococcus flavefaciens FD-1	Mutation(s): 0  Gene Names: scaE
UniProt
Find proteins for A0AEF6 (Ruminococcus flavefaciens) Explore A0AEF6  Go to UniProtKB:  A0AEF6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Group 2 dockerin from R. flavefaciens FD-1	B, C	72	Ruminococcus flavefaciens FD-1	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth B], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.39	α = 90
b = 142.39	β = 90
c = 57.596	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Bule, P., Carvalho, A.L., Najmudin, S.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/00276/2020, LA/P/0059/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release