7RTZ | pdb_00007rtz

X-ray crystallographic structure of a beta-hairpin peptide derived from amyloid beta 14-40

PDB DOI: https://doi.org/10.2210/pdb7RTZ/pdb

Classification: DE NOVO PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2021-08-16 Released: 2022-08-31
Deposition Author(s): Samdin, T.D., Kreutzer, A.G., Nowick, J.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.293 (Depositor), 0.291 (DCC)
R-Value Work:
0.263 (Depositor), 0.264 (DCC)
R-Value Observed:
0.266 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7RTZ

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

Literature

A beta-Barrel-Like Tetramer Formed by a beta-Hairpin Derived From A beta

Samdin, T.D., Jones, C.R., Guaglianone, G., Kreutzer, A.G., Freites, J.A., Wierzbicki, M., Nowick, J.S.

(2023) Chem Sci

DOI: https://doi.org/10.1039/D3SC05185D

Macromolecule Content

Total Structure Weight: 5.3 kDa
Atom Count: 376
Modeled Residue Count: 48
Deposited Residue Count: 48
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid-beta protein 40	A, B	24	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067 Go to UniProtKB: P05067
PHAROS: P05067 GTEx: ENSG00000142192
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05067
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN Query on ORN	A, B	L-PEPTIDE LINKING	C₅ H₁₂ N₂ O₂		ALA
SAR Query on SAR	A, B	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.293 (Depositor), 0.291 (DCC)
R-Value Work: 0.263 (Depositor), 0.264 (DCC)
R-Value Observed: 0.266 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.327	α = 90
b = 44.327	β = 90
c = 64.427	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM097562
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-08-31
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-12-13
Changes: Database references

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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.