5CVI

Structure of the manganese regulator SloR

PDB DOI: https://doi.org/10.2210/pdb5CVI/pdb

Classification: Transcription regulator
Organism(s): Streptococcus mutans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-27 Released: 2015-08-12
Deposition Author(s): Nye, D., Glasfeld, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.258 (Depositor), 0.277 (DCC)
R-Value Work:
0.200 (Depositor), 0.210 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

SloR structure and DNA binding studies inform the SloR-SRE interaction in Streptococcus mutans

Spatafora, G., Corbett, J., Cornacchione, L.P., Daly, W.C., Galan-Donlo, D., Wysota, M., Tivnan, P., Collins, J., Nye, D., Levitz, T., Breyer, W.A., Glasfeld, A.

To be published.

Macromolecule Content

Total Structure Weight: 50.91 kDa
Atom Count: 3,519
Modelled Residue Count: 427
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SloR	A, B	215	Streptococcus mutans	Mutation(s): 0 Gene Names: sloR
UniProt
Find proteins for Q9KIJ2 (Streptococcus mutans) Explore Q9KIJ2 Go to UniProtKB: Q9KIJ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KIJ2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.258 (Depositor), 0.277 (DCC)
R-Value Work: 0.200 (Depositor), 0.210 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.432	α = 90
b = 60.432	β = 90
c = 298.78	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Nye, D.

Glasfeld, A.

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2020-02-26
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary