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- PDB-6kjk: Structure of the N-terminal domain of PorA -

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Basic information

Entry
Database: PDB / ID: 6kjk
TitleStructure of the N-terminal domain of PorA
ComponentsN-terminal domain of PorA (28-171)
KeywordsSIGNALING PROTEIN / T9SS cargo protein
Function / homologyT9SS C-terminal target domain-containing protein
Function and homology information
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsHanda, Y. / Sato, K. / Shoji, M. / Nakayama, K. / Imada, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H05504 Japan
CitationJournal: Sci Rep / Year: 2020
Title: PorA, a conserved C-terminal domain-containing protein, impacts the PorXY-SigP signaling of the type IX secretion system.
Authors: Yukitake, H. / Shoji, M. / Sato, K. / Handa, Y. / Naito, M. / Imada, K. / Nakayama, K.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-terminal domain of PorA (28-171)


Theoretical massNumber of molelcules
Total (without water)15,4981
Polymers15,4981
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6950 Å2
Unit cell
Length a, b, c (Å)67.300, 43.220, 48.590
Angle α, β, γ (deg.)90.000, 108.520, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

21A-301-

HOH

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Components

#1: Protein N-terminal domain of PorA (28-171)


Mass: 15498.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal GSH, a remnant of the His-tag.
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Strain: ATCC 33277 / Gene: PGN_0123 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2RGZ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 0.1M (NH4)2SO4, 26%(w/v) PEG-8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→46.1 Å / Num. obs: 31131 / % possible obs: 95.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.49 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1548 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→46.1 Å / SU ML: 0.1312 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1131
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1590 5.11 %Random
Rwork0.181 ---
obs0.1821 31128 95.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.19 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 145 1137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931026
X-RAY DIFFRACTIONf_angle_d1.0571395
X-RAY DIFFRACTIONf_chiral_restr0.1028161
X-RAY DIFFRACTIONf_plane_restr0.0075184
X-RAY DIFFRACTIONf_dihedral_angle_d3.5935592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.25941450.22612683X-RAY DIFFRACTION95.9
1.34-1.390.24991520.21322677X-RAY DIFFRACTION95.22
1.39-1.450.24041250.2172548X-RAY DIFFRACTION91.26
1.45-1.510.2271570.20282715X-RAY DIFFRACTION97.36
1.51-1.590.22891450.19472689X-RAY DIFFRACTION95.32
1.59-1.690.20671250.18942601X-RAY DIFFRACTION92.25
1.69-1.820.19781540.18112722X-RAY DIFFRACTION96.93
1.82-20.20371630.18192716X-RAY DIFFRACTION97
2-2.290.22291410.17642650X-RAY DIFFRACTION94.26
2.29-2.890.22191440.19022777X-RAY DIFFRACTION97.27
2.89-46.070.16651390.16252760X-RAY DIFFRACTION95.11

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