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), 0.254 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.254 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (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

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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

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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.