8HS7 | pdb_00008hs7

Crystal structure of Vesicle-associated membrane protein-associated protein SCS2 from yeast

PDB DOI: https://doi.org/10.2210/pdb8HS7/pdb

Classification: CELL ADHESION
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-17 Released: 2024-01-17
Deposition Author(s): Xu, T.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.261 (Depositor), 0.261 (DCC)
R-Value Work:
0.249 (Depositor), 0.249 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8HS7

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the major sperm protein domain of SCS2 from saccharomyces cerevisiae

Xu, T.

To be published.

Macromolecule Content

Total Structure Weight: 14.23 kDa
Atom Count: 1,047
Modeled Residue Count: 126
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vesicle-associated membrane protein-associated protein SCS2	A	126	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SCS2, YER120W
UniProt
Find proteins for P40075 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40075 Go to UniProtKB: P40075
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40075
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDT Query on EDT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C₁₀ H₁₆ N₂ O₈ KCXVZYZYPLLWCC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.261 (Depositor), 0.261 (DCC)
R-Value Work: 0.249 (Depositor), 0.249 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.689	α = 90
b = 68.689	β = 90
c = 56.374	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-01-17
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.