8C3K | pdb_00008c3k

PaaR2 N-terminal domin in complex with nanobody 33

PDB DOI: https://doi.org/10.2210/pdb8C3K/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli O157:H7, Lama glama
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-12-26 Released: 2024-01-10
Deposition Author(s): Loris, R., Prolic-Kalinsek, M.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.203 (Depositor), 0.200 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

PaaR2, the CI equivalent in Escherichia coli O157:H7 cryptic prophage CP-933P

Prolik-Kalinsek, M., Volkov, A., Loris, R.

To be published.

Macromolecule Content

Total Structure Weight: 21.61 kDa
Atom Count: 1,395
Modeled Residue Count: 171
Deposited Residue Count: 191
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage repressor protein CI	A	74	Escherichia coli O157:H7	Mutation(s): 0 Gene Names: ECs_2279
UniProt
Find proteins for Q8XAD6 (Escherichia coli O157:H7) Explore Q8XAD6 Go to UniProtKB: Q8XAD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8XAD6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 33	B	117	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.203 (Depositor), 0.200 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.143	α = 90
b = 67.143	β = 90
c = 69.707	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Prolic-Kalinsek, M.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G.0226.17N

Revision History (Full details and data files)

Version 1.0: 2024-01-10
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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.