6EBB

Crystal Structure of YycF homologue, crystals grown in Tris buffer

PDB DOI: https://doi.org/10.2210/pdb6EBB/pdb
Entry: 6EBB supersedes: 2A9Q

Classification: SIGNALING PROTEIN
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-08-06 Released: 2019-08-14
Deposition Author(s): Riboldi-Tunnicliffe, A., Panjikar, S., Williamson, R.M., Gabrielsen, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.255
R-Value Work: 0.211
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of YycF homologue, crystals grown in Tris buffer

Riboldi-Tunnicliffe, A., Panjikar, S.

To be published.

Macromolecule Content

Total Structure Weight: 13.6 kDa
Atom Count: 953
Modelled Residue Count: 118
Deposited Residue Count: 120
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	A	120	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: SP_1227
UniProt
Find proteins for A0A0H2UQ68 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UQ68 Go to UniProtKB: A0A0H2UQ68
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2UQ68
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.255
R-Value Work: 0.211
R-Value Observed: 0.213
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.563	α = 90
b = 93.324	β = 90
c = 37.456	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Riboldi-Tunnicliffe, A.

Williamson, R.M.

This entry supersedes: 2A9Q

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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 R01GM133198.