9V85 | pdb_00009v85

Superfolder GFP fused gp38 receptor binding domain of bacteriophage PP01

PDB DOI: https://doi.org/10.2210/pdb9V85/pdb

Classification: CELL ADHESION
Organism(s): Aequorea victoria, Escherichia phage PP01
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-05-29 Released: 2026-01-07
Deposition Author(s): Kanamaru, S., Otsuka, Y.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.208 (Depositor), 0.207 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural and functional insights into the interaction between an PP01 phage gp38 tail fiber tip and an Escherichia coli OmpC receptor

Kanamaru, S., Otsuka, Y.

To be published.

Macromolecule Content

Total Structure Weight: 101.12 kDa
Atom Count: 5,496
Modeled Residue Count: 667
Deposited Residue Count: 944
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Receptor-recognizing protein gp38	A, B [auth C]	472	Aequorea victoria, Escherichia phage PP01 This entity is chimeric	Mutation(s): 1 Gene Names: gfp, 38
UniProt
Find proteins for A0A059PIQ0 (Aequorea victoria) Explore A0A059PIQ0 Go to UniProtKB: A0A059PIQ0
Find proteins for A0A2Z5WK79 (Escherichia phage PP01) Explore A0A2Z5WK79 Go to UniProtKB: A0A2Z5WK79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	A0A2Z5WK79A0A059PIQ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth C] MOL2 format, chain C [auth A] MOL2 format, chain D [auth C] mmCIF format, chain C [auth A] mmCIF format, chain D [auth C]	C [auth A], D [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A, B [auth C]	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.208 (Depositor), 0.207 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.217	α = 90
b = 172.217	β = 90
c = 79.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Japan	25440066

Revision History (Full details and data files)

Version 1.0: 2026-01-07
Type: Initial release

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.