4L92 | pdb_00004l92

Structure of the RBP from lactococcal phage 1358 in complex with 2 GlcNAc molecules

• PDB DOI: https://doi.org/10.2210/pdb4L92/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Lactococcus phage 1358
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-06-18 Released: 2014-04-30 
• Deposition Author(s): Farenc, C., Spinelli, S., Bebeacua, C., Tremblay, D., Orlov, I., Blangy, S., Klaholz, B.P., Moineau, S., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

A Virulent Siphophage CyoEM Structure and Host Recognition and Infection Mechanism

Farenc, C., Spinelli, S., Bebeacua, C., Tremblay, D., Orlov, I., Blangy, S., Klaholz, B.P., Moineau, S., Cambillau, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.71 kDa 
• Atom Count: 6,959 
• Modeled Residue Count: 781 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor Binding Protein	A, B	393	Lactococcus phage 1358	Mutation(s): 0  Gene Names: ORF20
UniProt
Find proteins for D3W0F1 (Lactococcus phage 1358) Explore D3W0F1  Go to UniProtKB:  D3W0F1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	C [auth A]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	D [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.64	α = 90
b = 165.64	β = 90
c = 165.64	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Farenc, C., Spinelli, S., Bebeacua, C., Tremblay, D., Orlov, I., Blangy, S., Klaholz, B.P., Moineau, S., Cambillau, C.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary