2YPS | pdb_00002yps

Crystal structure of the PX domain of human sorting nexin 3

PDB DOI: https://doi.org/10.2210/pdb2YPS/pdb

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

Deposited: 2012-10-31 Released: 2013-03-20
Deposition Author(s): Canning, P., Kiyani, W., Froese, D.S., Krojer, T., Strain-Damerell, C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Yue, W.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.255 (Depositor), 0.250 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Px Domain of Human Sorting Nexin 3

Canning, P., Froese, D.S., Krojer, T., Strain-Damerell, C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Yue, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 62.61 kDa
Atom Count: 3,102
Modeled Residue Count: 408
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SORTING NEXIN-3	A, B, C, D	134	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O60493 (Homo sapiens) Explore O60493 Go to UniProtKB: O60493
PHAROS: O60493 GTEx: ENSG00000112335
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60493
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.255 (Depositor), 0.250 (DCC)
R-Value Work: 0.211 (Depositor), 0.210 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.84	α = 90
b = 81.7	β = 90
c = 184.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Strain-Damerell, C.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Other, Refinement description

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.