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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.204 (Depositor), 0.207 (DCC)
R-Value Work:
0.180 (Depositor), 0.187 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

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

Spinelli, S., Moineau, S., Cambillau, C.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3W0F1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GN1 Query on GN1 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose C₈ H₁₆ N O₉ P FZLJPEPAYPUMMR-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.204 (Depositor), 0.207 (DCC)
R-Value Work: 0.180 (Depositor), 0.187 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.