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- PDB-9biz: Crystal structure of the periplasmic domain of IgaA from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 9biz
TitleCrystal structure of the periplasmic domain of IgaA from Klebsiella pneumoniae
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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 23, 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


Theoretical massNumber of molelcules
Total (without water)29,8781
Polymers29,8781
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.514, 146.443, 52.981
Angle α, β, γ (deg.)90.000, 120.527, 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-763-

HOH

21A-809-

HOH

31A-815-

HOH

41A-822-

HOH

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Components

#1: Protein Intracellular growth attenuator protein igaA


Mass: 29877.654 Da / Num. of mol.: 1 / Fragment: periplasmic domain (UNP residues 373-645)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: igaA / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA35H6S5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 4.73 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.0 M lithium sulfate, 0.1 M Bis-Tris, pH 7.0

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Data collection

DiffractionMean temperature: 80 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 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17504 / % possible obs: 94.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 57.42 Å2 / Rpim(I) all: 0.103 / Net I/σ(I): 1.05
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 649 / CC1/2: 0.503

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX1.17.1_3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39 Å / SU ML: 0.2839 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.6678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 849 5.11 %
Rwork0.1947 15759 -
obs0.1967 16608 89.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 0 129 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012057
X-RAY DIFFRACTIONf_angle_d1.05452803
X-RAY DIFFRACTIONf_chiral_restr0.0532332
X-RAY DIFFRACTIONf_plane_restr0.0066366
X-RAY DIFFRACTIONf_dihedral_angle_d22.7287756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.3348990.27791800X-RAY DIFFRACTION62.1
2.66-2.860.3171340.2712540X-RAY DIFFRACTION87.24
2.86-3.150.29621470.23822855X-RAY DIFFRACTION97.85
3.15-3.610.24261570.2112851X-RAY DIFFRACTION98.14
3.61-4.540.20531450.1692872X-RAY DIFFRACTION97.54
4.54-390.2111670.17472841X-RAY DIFFRACTION96.53
Refinement TLS params.Method: refined / Origin x: 3.97628375098 Å / Origin y: 0.994053870875 Å / Origin z: 14.1195750345 Å
111213212223313233
T0.548106015981 Å20.0655470001172 Å20.155148412773 Å2-0.470643725512 Å20.0714995926566 Å2--0.502257315624 Å2
L1.04074757755 °2-2.51256214165 °21.18785965685 °2-5.77003428261 °2-1.68003647419 °2--0.399554868699 °2
S-0.0162964264785 Å °-0.0533147174431 Å °-0.200218708483 Å °0.268669973513 Å °0.0525751029828 Å °0.344517541833 Å °-0.064746167117 Å °-0.0493151919792 Å °-0.0561435180327 Å °
Refinement TLS groupSelection details: all

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