6EBR | pdb_00006ebr

Activation of RR02 bound to BeF3

PDB DOI: https://doi.org/10.2210/pdb6EBR/pdb

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

Deposited: 2018-08-06 Released: 2019-11-13
Deposition Author(s): Riboldi-Tunnicliffe, A., Panjikar, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.199 (Depositor), 0.197 (DCC)
R-Value Work:
0.169 (Depositor), 0.178 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Activation of RR02 bound to BeF3

Riboldi-Tunnicliffe, A.

To be published.

Macromolecule Content

Total Structure Weight: 13.72 kDa
Atom Count: 1,059
Modeled Residue Count: 118
Deposited Residue Count: 120
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UQ68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEF Query on BEF 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]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.199 (Depositor), 0.197 (DCC)
R-Value Work: 0.169 (Depositor), 0.178 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.705	α = 90
b = 93.404	β = 90
c = 37.611	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Riboldi-Tunnicliffe, A.

Revision History (Full details and data files)

Version 1.0: 2019-11-13
Type: Initial release
Version 1.1: 2022-05-04
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Refinement description

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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.