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- PDB-9biy: Crystal structure of the periplasmic domain of IgaA from Escheric... -

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Basic information

Entry
Database: PDB / ID: 9biy
TitleCrystal structure of the periplasmic domain of IgaA from Escherichia coli
Components
  • Intracellular growth attenuator protein igaA
  • Outer membrane lipoprotein RcsF
KeywordsSIGNALING PROTEIN / Periplasmic protein / signal transduction / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyIntracellular growth attenuator IgaA / Intracellular growth attenuator protein IgaA / Outer membrane lipoprotein RcsF / RcsF lipoprotein / periplasmic side of cell outer membrane / intracellular signal transduction / plasma membrane / Outer membrane lipoprotein RcsF / Intracellular growth attenuator protein igaA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWatanabe, N. / Savchenko, A. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Structure / Year: 2024
Title: Molecular insights into the initiation step of the Rcs signaling pathway.
Authors: Watanabe, N. / Savchenko, A.
History
DepositionApr 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intracellular growth attenuator protein igaA
B: Outer membrane lipoprotein RcsF


Theoretical massNumber of molelcules
Total (without water)39,2322
Polymers39,2322
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-9 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.382, 38.266, 120.068
Angle α, β, γ (deg.)90.000, 94.965, 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

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Components

#1: Protein Intracellular growth attenuator protein igaA


Mass: 29840.906 Da / Num. of mol.: 1 / Fragment: periplasmic domain (UNP residues 203-476)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GP975_16005 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T5ZEU4
#2: Protein Outer membrane lipoprotein RcsF


Mass: 9390.660 Da / Num. of mol.: 1 / Fragment: UNP residues 49-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rcsF, NCTC10865_05029 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376RNX1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2 M potassium citrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→39.87 Å / Num. obs: 30909 / % possible obs: 93.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.51 Å2 / Rpim(I) all: 0.063 / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5234 / Rpim(I) all: 1.882

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→39.87 Å / SU ML: 0.278 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2757 1583 5.16 %
Rwork0.2399 29119 -
obs0.2418 30702 92.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 0 254 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712661
X-RAY DIFFRACTIONf_angle_d0.93373619
X-RAY DIFFRACTIONf_chiral_restr0.0516421
X-RAY DIFFRACTIONf_plane_restr0.0057478
X-RAY DIFFRACTIONf_dihedral_angle_d21.2854981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.4433890.37231629X-RAY DIFFRACTION57.32
1.86-1.920.4271210.36672067X-RAY DIFFRACTION72.76
1.92-20.36161380.33882724X-RAY DIFFRACTION95.24
2-2.090.36161440.31442818X-RAY DIFFRACTION98.73
2.09-2.20.31881750.29422771X-RAY DIFFRACTION98.4
2.2-2.340.2911590.27022766X-RAY DIFFRACTION96.95
2.34-2.520.27531500.26252864X-RAY DIFFRACTION99.05
2.52-2.780.32511570.26192792X-RAY DIFFRACTION97.62
2.78-3.180.33041400.25042886X-RAY DIFFRACTION99.41
3.18-40.24871380.20472867X-RAY DIFFRACTION98.01
4-39.870.20761720.19022935X-RAY DIFFRACTION98.35

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