5WAY | pdb_00005way

MgaSpn protein, Mga regulator from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb5WAY/pdb

Classification: TRANSCRIPTION
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2017-06-27 Released: 2017-07-05
Deposition Author(s): Osipiuk, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5WAY

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

Literature

MgaSpn protein, Mga regulator from Streptococcus pneumoniae

Osipiuk, J.

To be published.

Macromolecule Content

Total Structure Weight: 119.68 kDa
Atom Count: 8,338
Modeled Residue Count: 959
Deposited Residue Count: 1,002
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional activator	A, B	501	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: atxA, ERS020151_00445, ERS021360_00762, ERS455152_01375
UniProt
Find proteins for Q97P44 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q97P44 Go to UniProtKB: Q97P44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97P44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K 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]	POTASSIUM ION K NPYPAHLBTDXSSS-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: 2.09 Å
R-Value Free: 0.232 (Depositor), 0.235 (DCC)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.118	α = 90
b = 106.256	β = 101.76
c = 100.213	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-07-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-05
Type: Initial release
Version 1.1: 2024-03-13
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.