8QPC

18mer DNA mimic Foldamer with an Aromatic linker in complex with Sac7d V26A/M29A protein

PDB DOI: https://doi.org/10.2210/pdb8QPC/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Sulfolobus acidocaldarius, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-10-01 Released: 2023-11-08
Deposition Author(s): Deepak, D., Corvaglia, V., Wu, J., Huc, I.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free: 0.348
R-Value Work: 0.336
R-Value Observed: 0.336

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Literature

DNA-Mimic Foldamer Recognition of a Chromosomal Protein

Deepak, D., Corvaglia, V., Wu, J., Allmendinger, L., Huc, I.

To be published.

Macromolecule Content

Total Structure Weight: 12.66 kDa
Atom Count: 812
Modelled Residue Count: 83
Deposited Residue Count: 86
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein 7b	A [auth AA]	66	Sulfolobus acidocaldarius	Mutation(s): 2 Gene Names: Saci_0064
UniProt
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore P13123 Go to UniProtKB: P13123
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13123
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide	B	10	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
N-[2-(2-methyl-1,3-dioxolan-2-yl)phenyl]-2-{[5-(trifluoromethyl)pyridin-2-yl]amino}pyridine-4-carboxamide	C	10	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DBU Query on DBU	B	PEPTIDE LINKING	C₄ H₇ N O₂		THR
V4F Query on V4F	B	PEPTIDE LINKING	C₁₂ H₁₃ N₂ O₆ P		V4F
V53 Query on V53	B	PEPTIDE LINKING	C₁₁ H₁₁ N₂ O₆ P		ES1

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free: 0.348
R-Value Work: 0.336
R-Value Observed: 0.336
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.907	α = 90
b = 70.907	β = 90
c = 121.997	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-08

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	325871075 (CRC1309-C7)
European Research Council (ERC)	European Union	ERC-2021-ADG-320892

Revision History (Full details and data files)

Version 1.0: 2023-11-08
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 3.0: 2024-05-01
Changes: Atomic model, Polymer sequence

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.