7PVK

X-ray structure of dimeric PorX (T272A mutant), in complex with pGpG.

PDB DOI: https://doi.org/10.2210/pdb7PVK/pdb
NAKB: 7PVK

Classification: SIGNALING PROTEIN
Organism(s): Porphyromonas gingivalis W83, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-10-04 Released: 2022-12-14
Deposition Author(s): Schmitz, C.A., Madej, M., Potempa, J., Sola, M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.223
R-Value Work: 0.194

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors

Schmitz, C., Madej, M., Nowakowska, Z., Cuppari, A., Jacula, A., Ksiazek, M., Mikruta, K., Wisniewski, J., Pudelko-Malik, N., Saran, A., Zeytuni, N., Mlynarz, P., Lamont, R.J., Uson, I., Siksnys, V., Potempa, J., Sola, M.

(2022) Nucleic Acids Res 50: 12558-12577

DOI: https://doi.org/10.1093/nar/gkac1103

Macromolecule Content

Total Structure Weight: 253.89 kDa
Atom Count: 17,799
Modelled Residue Count: 2,060
Deposited Residue Count: 2,100
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator	A, B, C, D	523	Porphyromonas gingivalis W83	Mutation(s): 1 Gene Names: PG_0928
UniProt
Find proteins for Q7MVV4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVV4 Go to UniProtKB: Q7MVV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MVV4
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
pGpG	E, F, G, H	2	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] HA [auth C] IA [auth C] JA [auth C] AA [auth B], BA [auth B], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], SA [auth D], TA [auth D], UA [auth D], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
BEF (Subject of Investigation/LOI) Query on BEF Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain J [auth A] SDF format, chain QA [auth D] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain V [auth B]	FA [auth C], J [auth A], QA [auth D], V [auth B]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain FA [auth C] Focus chain J [auth A] Focus chain QA [auth D] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain J [auth A] Focus chain QA [auth D] Focus chain V [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain GA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain RA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D]	DA [auth B] GA [auth C] K [auth A] L [auth A] NA [auth C] DA [auth B], GA [auth C], K [auth A], L [auth A], NA [auth C], OA [auth C], RA [auth D], W [auth B], WA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain RA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Interactions & Density Focus chain DA [auth B] Focus chain GA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain RA [auth D] Focus chain W [auth B] Focus chain WA [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain MA [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain VA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain VA [auth D]	CA [auth B] MA [auth C] R [auth A] S [auth A] T [auth A] CA [auth B], MA [auth C], R [auth A], S [auth A], T [auth A], VA [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain MA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain VA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain MA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain VA [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain I [auth A] SDF format, chain PA [auth D] SDF format, chain U [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain U [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain U [auth B]	EA [auth C], I [auth A], PA [auth D], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain I [auth A] Focus chain PA [auth D] Focus chain U [auth B] Interactions & Density Focus chain EA [auth C] Focus chain I [auth A] Focus chain PA [auth D] Focus chain U [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.223
R-Value Work: 0.194
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.63	α = 90
b = 103.77	β = 98.5
c = 132.21	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Spain	--
Other government	Poland	--

Revision History (Full details and data files)

Version 1.0: 2022-12-14
Type: Initial release
Version 2.0: 2023-01-04
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-01-11
Changes: Database references