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- PDB-6od1: IraD-bound to RssB D58P variant -

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Basic information

Entry
Database: PDB / ID: 6od1
TitleIraD-bound to RssB D58P variant
Components
  • Anti-adapter protein IraD
  • Regulator of RpoS
KeywordsSIGNALING PROTEIN / response regulator / ClpXP adaptor / anti-adaptor / DNA damage / Gp25
Function / homology
Function and homology information


anti-sigma factor antagonist activity / phosphorelay signal transduction system / positive regulation of proteolysis / negative regulation of protein catabolic process / cellular response to oxidative stress / regulation of gene expression / DNA damage response / cytoplasm
Similarity search - Function
Anti-adapter protein, IraD / Regulator of RpoS / IraD/Gp25-like / Baseplate wedge protein gp25 / PPM-type phosphatase-like domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Anti-adapter protein IraD / Regulator of RpoS
Similarity search - Component
Biological speciesEscherichia coli 907672 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDeaconescu, A.M. / Dorich, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121975 United States
CitationJournal: Genes Dev. / Year: 2019
Title: Structural basis for inhibition of a response regulator of sigmaSstability by a ClpXP antiadaptor.
Authors: Dorich, V. / Brugger, C. / Tripathi, A. / Hoskins, J.R. / Tong, S. / Suhanovsky, M.M. / Sastry, A. / Wickner, S. / Gottesman, S. / Deaconescu, A.M.
History
DepositionMar 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of RpoS
B: Anti-adapter protein IraD


Theoretical massNumber of molelcules
Total (without water)50,4572
Polymers50,4572
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-12 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.938, 55.938, 300.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Regulator of RpoS


Mass: 37320.125 Da / Num. of mol.: 1 / Mutation: D58P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 907672 (bacteria) / Gene: rssB, HMPREF1595_01509 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: V0SNG0
#2: Protein Anti-adapter protein IraD


Mass: 13136.972 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: iraD, yjiD, b4326, JW5782 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39375
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence of IraD that was expressed in Ecoli was: ...The sequence of IraD that was expressed in Ecoli was: MGSSHHHHHHSSGLEVLFQGPHMKTSSLRKSVCSDLLTLFNSPHSALPSLLVSGMPEWQVHNPSDKHLQSWYCRQLRSALLFHEPRIAALQVNLKEAYCHTLAISLEIMLYHDDEPLTFDLVWDNGGWRSATLENVS IraD protein that was crystallized was obtain by digesting the sequence above with protease and is: MKTSSLRKSVCSDLLTLFNSPHSALPSLLVSGMPEWQVHNPSDKHLQSWYCRQLRSALLFHEPRIAALQVNLKEAYCHTLAISLEIMLYHDDEPLTFDLVWDNGGWRSATLENVS

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, PEG 8000, Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.1 Å / Num. obs: 3053 / % possible obs: 96.9 % / Observed criterion σ(I): 1.95 / Redundancy: 7.4 % / Net I/σ(I): 25
Reflection shellResolution: 2.05→2.1 Å / Num. unique obs: 5272

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→29.08 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1816 5.57 %1
Rwork0.2 ---
obs0.2025 32605 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 0 109 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083496
X-RAY DIFFRACTIONf_angle_d0.9384752
X-RAY DIFFRACTIONf_dihedral_angle_d5.0632112
X-RAY DIFFRACTIONf_chiral_restr0.057548
X-RAY DIFFRACTIONf_plane_restr0.006615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.29661300.28822178X-RAY DIFFRACTION92
2.0541-2.11450.31591350.26822289X-RAY DIFFRACTION96
2.1145-2.18270.30911370.25492320X-RAY DIFFRACTION97
2.1827-2.26070.30081370.24142318X-RAY DIFFRACTION97
2.2607-2.35120.26281380.22642338X-RAY DIFFRACTION98
2.3512-2.45810.28751380.22882350X-RAY DIFFRACTION97
2.4581-2.58770.28981370.22942324X-RAY DIFFRACTION97
2.5877-2.74970.27961380.22552341X-RAY DIFFRACTION96
2.7497-2.96180.24931390.21752368X-RAY DIFFRACTION97
2.9618-3.25950.27121380.21532354X-RAY DIFFRACTION96
3.2595-3.73030.22611430.19112416X-RAY DIFFRACTION97
3.7303-4.69660.22521480.16452506X-RAY DIFFRACTION100
4.6966-29.0830.21611580.18352687X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.51751.3573-0.61192.3937-1.85645.2104-0.16010.44180.2315-0.16830.35710.2875-0.1237-0.8337-0.14270.35740.0032-0.10020.62680.05340.345915.36555.2652128.6252
25.00531.2106-0.12696.04682.47826.1172-0.05090.00290.88620.6674-0.6540.2876-0.7946-0.61080.65840.65610.0225-0.15370.53140.04360.43127.601417.8661135.105
35.2811-2.85174.61424.5519-3.01856.6669-0.6133-0.42880.67470.1611-0.028-0.0453-1.4447-0.68230.41870.66240.1538-0.09730.4185-0.04130.424340.775719.9726152.9295
42.7976-1.30522.28251.7892-0.59724.9828-0.0467-0.1178-0.1226-0.04090.1220.235-0.2855-0.2579-0.03320.2864-0.0491-0.06990.27180.09540.322543.95347.064146.2164
59.28073.87490.48982.59672.30324.7498-1.19281.437-0.2352-0.96560.8594-0.45430.22850.34930.41720.68010.04170.05170.79440.03840.557145.34878.5327110.1636
62.8968-2.24942.73565.9263-4.44773.88660.13870.5004-0.021-1.52440.45950.25340.2179-0.4945-0.21870.7047-0.0326-0.151.06890.0920.45825.110211.0553107.809
79.7601-3.763.54645.1326-0.08094.27460.03720.01360.401-0.32150.08790.1518-0.1294-0.4021-0.12170.4072-0.039-0.1330.5270.16250.34729.285913.8317118.145
85.6579-4.25615.38964.9548-3.95675.17510.17090.680.7486-0.28140.005-0.3531-0.2512-0.16990.14890.48670.0602-0.0520.53930.17330.409239.883213.4926118.8253
98.97865.08485.10633.0783.09433.2515-1.12491.67693.0415-3.281-0.24830.5831-2.4896-0.62891.42331.54510.1549-0.33281.11380.38811.275131.027524.0615104.2987
104.2242-4.92474.36067.3623-4.53624.6823-0.42571.08560.86040.4230.48110.1245-1.513-0.50640.90910.65480.0113-0.05330.83190.28690.384838.613218.4572113.472
111.42751.1067-1.20294.5095-4.56356.0028-0.337-0.07171.00460.4544-0.5384-1.5389-1.89141.89540.49010.7206-0.2-0.17990.87160.26210.703450.511914.8832121.6137
125.26912.22126.06961.16172.71987.4685-0.69770.2844-0.4436-0.50640.28590.027-0.9517-0.56450.21810.7576-0.0983-0.1431.00520.22340.540938.90316.5959107.7021
130.1386-0.892-0.09085.79110.59270.0574-0.36161.90721.2004-2.8958-0.6422-0.4105-0.2324-0.01880.72830.82870.0917-0.10271.58740.23180.579535.554213.6063100.4474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 337 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 34 )
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 58 )
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 76 )
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 87 )
9X-RAY DIFFRACTION9chain 'B' and (resid 88 through 95 )
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 109 )
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 116 )
13X-RAY DIFFRACTION13chain 'B' and (resid 117 through 124 )

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