6XOD | pdb_00006xod

Crystal structure of the PEX4-PEX22 protein complex from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb6XOD/pdb

Classification: LIGASE/TRANSPORT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-07-06 Released: 2021-07-14
Deposition Author(s): Olmos Jr., J.L., Bradford, S.E., Miller, M.D., Xu, W., Wright, Z.J., Bartel, B., Phillips Jr., G.N.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.237 (Depositor), 0.241 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex-Insights Into Ubiquitination at the Peroxisomal Membrane

Traver, M.S., Bradford, S.E., Olmos, J.L., Wright, Z.J., Miller, M.D., Xu, W., Phillips, G.N., Bartel, B.

(2022) Front Cell Dev Biol 10: 838923-838923

DOI: https://doi.org/10.3389/fcell.2022.838923

Macromolecule Content

Total Structure Weight: 38.22 kDa
Atom Count: 2,693
Modeled Residue Count: 320
Deposited Residue Count: 339
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PEROXIN-4	A	164	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PEX4, UBC21, At5g25760, F18A17.10 EC: 2.3.2.23
UniProt
Find proteins for Q8LGF7 (Arabidopsis thaliana) Explore Q8LGF7 Go to UniProtKB: Q8LGF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8LGF7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome biogenesis protein 22	B	175	Arabidopsis thaliana	Mutation(s): 0 Gene Names: PEX22, At3g21865, MSD21.24
UniProt
Find proteins for Q9LSX7 (Arabidopsis thaliana) Explore Q9LSX7 Go to UniProtKB: Q9LSX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LSX7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.237 (Depositor), 0.241 (DCC)
R-Value Work: 0.194 (Depositor)
R-Value Observed: 0.196 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.389	α = 90
b = 100.484	β = 90
c = 112.092	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data processing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM130338
Robert A. Welch Foundation	United States	C1309
National Science Foundation (NSF, United States)	United States	GRFP 1450681
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115261
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA217255

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 2.0: 2022-03-02
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-10-18
Changes: Data collection, Refinement description