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- PDB-8gkv: Crystal structure of anti-adaptor IraP that regulates RpoS proteolysis -

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Basic information

Entry
Database: PDB / ID: 8gkv
TitleCrystal structure of anti-adaptor IraP that regulates RpoS proteolysis
ComponentsAnti-adapter protein IraP
KeywordsGENE REGULATION / alpha helix
Function / homologySigma-S stabilisation anti-adaptor protein / Sigma-S stabilisation anti-adaptor protein / anti-sigma factor antagonist activity / cellular response to phosphate starvation / negative regulation of protein catabolic process / cytoplasm / Anti-adapter protein IraP
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.351 Å
Model detailsLeucine zipper-like protein
AuthorsShaw, G.X. / Gan, J. / Suburaman, P. / Battesti, A. / Zhou, Y.N. / Wickner, S. / Gottesman, S. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: to be published
Title: Structural and functional study of anti-adaptor IraP-mediated regulation of RpoS proteolysis
Authors: Tripathi, A. / Hoskins, J. / Shaw, G.X. / Gan, J. / Tong, S. / Battesti, A. / Jenkins, L.M. / Ji, X. / Wickner, S. / Gottesman, S.
History
DepositionMar 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-adapter protein IraP
B: Anti-adapter protein IraP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,92715
Polymers20,0972
Non-polymers83013
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-81 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.335, 57.013, 48.629
Angle α, β, γ (deg.)90.000, 129.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-218-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Anti-adapter protein IraP


Mass: 10048.501 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-86 / Mutation: C23S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: iraP, yaiB, b0382, JW0373 / Plasmid: IraPC23S / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AAN9

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Non-polymers , 5 types, 43 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 Å3/Da / Density % sol: 38.65 % / Mosaicity: 0.806 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Tri-Na citrate, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2009 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: k+l,h+l,-l / Fraction: 0.17
ReflectionResolution: 2.35→30 Å / Num. obs: 6391 / % possible obs: 95.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Χ2: 1.093 / Net I/σ(I): 16 / Num. measured all: 21575
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.35-2.432.60.1565140.992177.4
2.43-2.532.80.1515951.021188.9
2.53-2.653.10.1276421.026196.7
2.65-2.793.50.1266630.998199.4
2.79-2.963.60.0966631.018199.8
2.96-3.193.70.0716651.0721100
3.19-3.513.70.0556561.126199.2
3.51-4.023.50.0446611.192198.1
4.02-5.063.40.0366461.225196.3
5.06-303.50.0356861.179198.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.351→29.064 Å / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.48 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2386 710 11.11 %
Rwork0.2149 5745 -
obs0.2238 6390 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.6 Å2 / Biso mean: 55.296 Å2 / Biso min: 21.23 Å2
Refinement stepCycle: final / Resolution: 2.351→29.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms656 0 65 30 751
Biso mean--76.52 57.63 -
Num. residues----84
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006690
X-RAY DIFFRACTIONf_angle_d0.745916
X-RAY DIFFRACTIONf_chiral_restr0.031110
X-RAY DIFFRACTIONf_plane_restr0.002113
X-RAY DIFFRACTIONf_dihedral_angle_d18.038274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3524-2.53380.28891110.2651999111075
2.5338-2.78830.26441310.23631176130788
2.7883-3.19090.2841320.23131191132390
3.1909-4.01650.22981320.20591184131689
4.0165-22.69990.22531330.21351195132888

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