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- PDB-7pv7: Crystal structure of dimeric Porphyromonas gingivalis PorX, a typ... -

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Basic information

Entry
Database: PDB / ID: 7pv7
TitleCrystal structure of dimeric Porphyromonas gingivalis PorX, a type 9 secretion system response regulator.
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / Response regulator / Type 9 Secretion System / PglZ / Phosphodiesterase
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
PglZ domain / PglZ domain / Alkaline-phosphatase-like, core domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / FORMIC ACID / Response regulator
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsSchmitz, C.A. / Madej, M. / Potempa, J. / Sola, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
Other government
Other government Poland
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors.
Authors: 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. / ...Authors: 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.
History
DepositionOct 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Response regulator
C: Response regulator
B: Response regulator
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,15846
Polymers248,5464
Non-polymers2,61342
Water21,0051166
1
D: Response regulator
C: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,38321
Polymers124,2732
Non-polymers1,11019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-145 kcal/mol
Surface area41670 Å2
MethodPISA
2
B: Response regulator
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,77625
Polymers124,2732
Non-polymers1,50323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-156 kcal/mol
Surface area42240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.830, 77.080, 138.730
Angle α, β, γ (deg.)82.260, 81.360, 76.410
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules DCBA

#1: Protein
Response regulator /


Mass: 62136.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria)
Strain: ATCC BAA-308 / W83 / Gene: PG_0928 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MVV4

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Non-polymers , 6 types, 1208 molecules

#2: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM glycine pH 8.0, 100 mM sodium formate and a PEG-mixture of 20K, 10K, 8K and 6K (1.5% each)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97893 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.41→68.4 Å / Num. obs: 92407 / % possible obs: 97.91 % / Redundancy: 3.6 % / Biso Wilson estimate: 49.34 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1264 / Rpim(I) all: 0.07766 / Rrim(I) all: 0.149 / Net I/σ(I): 6.45
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.8829 / Num. unique obs: 8754 / CC1/2: 0.613 / CC star: 0.872 / Rpim(I) all: 0.5407 / Rrim(I) all: 1.039 / % possible all: 93.11

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→68.4 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2155 --
Rwork0.1857 --
obs-92407 97.91 %
Displacement parametersBiso max: 307.46 Å2 / Biso mean: 61.04 Å2 / Biso min: 21.91 Å2
Refinement stepCycle: LAST / Resolution: 2.41→68.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16961 0 143 1166 18270

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