2A9O | pdb_00002a9o

Crystal structures of an activated YycF homologue, the essential response regulator from S.pneumoniae in complex with BeF3 and the effect of pH on BeF3 binding, possible phosphate in the active site

PDB DOI: https://doi.org/10.2210/pdb2A9O/pdb

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

Deposited: 2005-07-12 Released: 2006-09-26
Deposition Author(s): Riboldi-Tunnicliffe, A., Isaacs, N.W., Mitchell, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.236 (Depositor), 0.216 (DCC)
R-Value Work:
0.192 (Depositor)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structures of an activated YycF homologue, the essential response regulator from S.pneumoniae in complex with BeF3 and the effect of pH on BeF3 binding, possible phosphate in the active site.

Riboldi-Tunnicliffe, A., Isaacs, N.W., Mitchell, T.J.

To be published.

Macromolecule Content

Total Structure Weight: 13.72 kDa
Atom Count: 1,024
Modeled Residue Count: 117
Deposited Residue Count: 120
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator	A	120	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for Q9S1K0 (Streptococcus pneumoniae) Explore Q9S1K0 Go to UniProtKB: Q9S1K0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9S1K0
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain C [auth A]
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.236 (Depositor), 0.216 (DCC)
R-Value Work: 0.192 (Depositor)
R-Value Observed: 0.195 (Depositor)

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
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-09-26

Deposition Author(s):

Riboldi-Tunnicliffe, A.

Revision History (Full details and data files)

Version 1.0: 2006-09-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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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.