4RGG | pdb_00004rgg

Structure of the lactococcal phage 1358 receptor binding protein in complex with GlcNAc-1P

• PDB DOI: https://doi.org/10.2210/pdb4RGG/pdb

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


• Deposited: 2014-09-30 Released: 2014-10-15 
• Deposition Author(s): Spinelli, S., Moineau, S., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of the 1358 lactococcal phage RBP in complex with GlcNAc-1P

Spinelli, S., 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: 87.29 kDa 
• Atom Count: 6,596 
• Modeled Residue Count: 780 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phage structural 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GN1	C [auth A], D [auth B]	2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose C8 H16 N O9 P FZLJPEPAYPUMMR-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.91	α = 90
b = 165.91	β = 90
c = 165.91	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Spinelli, S., Moineau, S., Cambillau, C.

Revision History  

• Version 1.0: 2014-10-15
  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