9F2M | pdb_00009f2m

To be published

PDB DOI: https://doi.org/10.2210/pdb9F2M/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Marchantia polymorpha, Phytophthora infestans
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2024-04-23 Released: 2025-05-21
Deposition Author(s): Sanchez de Medina, V., Dagdas, Y.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.240 (Depositor), 0.239 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9F2M

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

Literature

To be published

Nn, N., Pp, P.

To be published.

Macromolecule Content

Total Structure Weight: 13.31 kDa
Atom Count: 1,056
Modeled Residue Count: 114
Deposited Residue Count: 114
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein	A	109	Marchantia polymorpha	Mutation(s): 0 Gene Names: MARPO_0001s0494
UniProt
Find proteins for A0A176W124 (Marchantia polymorpha subsp. ruderalis) Explore A0A176W124 Go to UniProtKB: A0A176W124
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A176W124
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RxLR effector protein 54	B [auth D]	5	Phytophthora infestans	Mutation(s): 0
UniProt
Find proteins for D0NBE6 (Phytophthora infestans (strain T30-4)) Explore D0NBE6 Go to UniProtKB: D0NBE6
Entity Groups
UniProt Group	D0NBE6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.240 (Depositor), 0.239 (DCC)
R-Value Work: 0.192 (Depositor), 0.192 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.23	α = 90
b = 36.23	β = 90
c = 69.59	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Sanchez de Medina, V.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101000981

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

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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.