4L97 | pdb_00004l97

Structure of the RBP of lactococcal phage 1358 in complex with glucose-1-phosphate

PDB DOI: https://doi.org/10.2210/pdb4L97/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.211 (Depositor), 0.222 (DCC)
R-Value Work:
0.179 (Depositor), 0.192 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 87.17 kDa
Atom Count: 6,498
Modeled Residue Count: 780
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
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
G1P Query on G1P 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]	1-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P HXXFSFRBOHSIMQ-VFUOTHLCSA-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: 2.61 Å
R-Value Free: 0.211 (Depositor), 0.222 (DCC)
R-Value Work: 0.179 (Depositor), 0.192 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.55	α = 90
b = 165.55	β = 90
c = 165.55	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
BUSTER	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: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 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.