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- PDB-9bj0: Crystal structure of the periplasmic domain of IgaA from Escheric... -

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Basic information

Entry
Database: PDB / ID: 9bj0
TitleCrystal structure of the periplasmic domain of IgaA from Escherichia coli
ComponentsIntracellular growth attenuator protein igaA
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 / plasma membrane / Intracellular growth attenuator protein igaA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intracellular growth attenuator protein igaA
B: Intracellular growth attenuator protein igaA


Theoretical massNumber of molelcules
Total (without water)59,1122
Polymers59,1122
Non-polymers00
Water1,20767
1
A: Intracellular growth attenuator protein igaA


Theoretical massNumber of molelcules
Total (without water)29,5561
Polymers29,5561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intracellular growth attenuator protein igaA


Theoretical massNumber of molelcules
Total (without water)29,5561
Polymers29,5561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.421, 94.179, 160.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-728-

HOH

21B-729-

HOH

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Components

#1: Protein Intracellular growth attenuator protein igaA


Mass: 29556.217 Da / Num. of mol.: 2 / Fragment: periplasmic domain (UNP residues 203-475)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GP975_16005 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8T5ZEU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2 M potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.64→40 Å / Num. obs: 20383 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 74.17 Å2 / Rrim(I) all: 0.083 / Net I/σ(I): 29.5
Reflection shellResolution: 2.65→2.74 Å / Num. unique obs: 1993 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→39.36 Å / SU ML: 0.3385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 1064 5.23 %
Rwork0.2162 19294 -
obs0.2182 20358 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.24 Å2
Refinement stepCycle: LAST / Resolution: 2.64→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 0 67 4049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01384057
X-RAY DIFFRACTIONf_angle_d1.22855521
X-RAY DIFFRACTIONf_chiral_restr0.0695641
X-RAY DIFFRACTIONf_plane_restr0.0077728
X-RAY DIFFRACTIONf_dihedral_angle_d22.24521483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.760.34581410.28992327X-RAY DIFFRACTION97.59
2.76-2.90.35561180.30792389X-RAY DIFFRACTION99.8
2.9-3.090.37421390.27982393X-RAY DIFFRACTION99.57
3.09-3.320.31451410.26722368X-RAY DIFFRACTION99.68
3.32-3.660.29481490.25442400X-RAY DIFFRACTION99.84
3.66-4.190.28491260.21442419X-RAY DIFFRACTION99.92
4.19-5.270.2371030.18732478X-RAY DIFFRACTION99.54
5.27-39.360.18971470.18562520X-RAY DIFFRACTION99.33

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