8TX9 | pdb_00008tx9

Nan Regulatory Protein (core isomerase domain) from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb8TX9/pdb

Classification: TRANSCRIPTION
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-08-23 Released: 2024-09-11
Deposition Author(s): Wood, D.M., Horne, C.R., Panjikar, S., Dobson, R.C.J.
Funding Organization(s): Royal Society of New Zealand, Ministry of Business, Innovation and Employment (New Zealand)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.271 (Depositor), 0.268 (DCC)
R-Value Work:
0.211 (Depositor), 0.217 (DCC)
R-Value Observed:
0.213 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure of isomerase domain of the nan-regulatory protein (NanR) from Streptococcus pneumoniae

Wood, D.M., Dobson, R.C.J.

To be published.

Macromolecule Content

Total Structure Weight: 132.13 kDa
Atom Count: 6,252
Modeled Residue Count: 746
Deposited Residue Count: 1,135
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MurR/RpiR family transcriptional regulator	A, B [auth C], C [auth D], D [auth B]	283	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for A0A064C3N8 (Streptococcus pneumoniae) Explore A0A064C3N8 Go to UniProtKB: A0A064C3N8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A064C3N8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BMX (Subject of Investigation/LOI) Query on BMX Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain I [auth D] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain I [auth D] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain I [auth D] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth C], I [auth D], K [auth B]	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose C₈ H₁₆ N O₉ P BRGMHAYQAZFZDJ-UOLFYFMNSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain I [auth D] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth D] SDF format, chain L [auth B] SDF format, chain H [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth D] MOL2 format, chain L [auth B] MOL2 format, chain H [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth D] mmCIF format, chain L [auth B] mmCIF format, chain H [auth C]	F [auth A], H [auth C], J [auth D], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth C] Focus chain J [auth D] Focus chain L [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.271 (Depositor), 0.268 (DCC)
R-Value Work: 0.211 (Depositor), 0.217 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.577	α = 90
b = 147.577	β = 90
c = 82.311	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	UOC1506
Ministry of Business, Innovation and Employment (New Zealand)	New Zealand	UOCX1706

Revision History (Full details and data files)

Version 1.0: 2024-09-11
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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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.