8RQT | pdb_00008rqt

Crystal structure of Pichia pastoris Pex8

PDB DOI: https://doi.org/10.2210/pdb8RQT/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Komagataella pastoris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-19 Released: 2025-01-29
Deposition Author(s): Ekal, L., Burgi, J., Chojnowski, G., WIlmanns, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.258 (Depositor), 0.257 (DCC)
R-Value Work:
0.212 (Depositor), 0.211 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Pichia pastoris Pex8

Ekal, L., Burgi, J., Chojnowski, G., WIlmanns, M.

To be published.

Macromolecule Content

Total Structure Weight: 81.08 kDa
Atom Count: 5,082
Modeled Residue Count: 621
Deposited Residue Count: 713
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal biogenesis factor 8	A	713	Komagataella pastoris	Mutation(s): 0 Gene Names: PEX8, PER3
UniProt
Find proteins for Q01962 (Komagataella pastoris) Explore Q01962 Go to UniProtKB: Q01962
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01962
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.258 (Depositor), 0.257 (DCC)
R-Value Work: 0.212 (Depositor), 0.211 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.149	α = 90
b = 87.842	β = 90
c = 153.093	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
Coot	model building
AutoSol	phasing
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	WI 1058/9-2

Revision History (Full details and data files)

Version 1.0: 2025-01-29
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.