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- PDB-8twd: Structure of IraM-bound RssB -

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Basic information

Entry
Database: PDB / ID: 8twd
TitleStructure of IraM-bound RssB
Components
  • Anti-adapter protein IraM
  • Regulator of RpoS
KeywordsSIGNALING PROTEIN / response regulator / ClpXP anti-adaptor
Function / homology
Function and homology information


sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / positive regulation of proteolysis / cellular response to starvation / protein destabilization / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription ...sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / positive regulation of proteolysis / cellular response to starvation / protein destabilization / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / cytosol / cytoplasm
Similarity search - Function
Anti-adapter protein IraM / Signal transduction protein PmrD superfamily / Regulator of RpoS / : / 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
ACETATE ION / Regulator of RpoS / Anti-adapter protein IraM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBrugger, C. / Deaconescu, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121975 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144124 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: IraM remodels the RssB segmented helical linker to stabilize sigma s against degradation by ClpXP.
Authors: Brugger, C. / Srirangam, S. / Deaconescu, A.M.
History
DepositionAug 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-adapter protein IraM
B: Anti-adapter protein IraM
C: Regulator of RpoS
D: Regulator of RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2035
Polymers93,1444
Non-polymers591
Water00
1
A: Anti-adapter protein IraM
C: Regulator of RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6313
Polymers46,5722
Non-polymers591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-30 kcal/mol
Surface area19180 Å2
MethodPISA
2
B: Anti-adapter protein IraM
D: Regulator of RpoS


Theoretical massNumber of molelcules
Total (without water)46,5722
Polymers46,5722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-29 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.664, 191.229, 96.985
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

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Components

#1: Protein Anti-adapter protein IraM


Mass: 9233.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: iraM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8SRD3
#2: Protein Regulator of RpoS


Mass: 37338.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rssB, hnr, sprE, ychL, b1235, JW1223 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEV1
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.5 120mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 2, 2018
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.3→49.33 Å / Num. obs: 18674 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 119.84 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 17.3
Reflection shellResolution: 3.3→3.56 Å / Num. unique obs: 3782 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→49.33 Å / SU ML: 0.3918 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 33.0358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2706 1722 10.07 %
Rwork0.2446 15381 -
obs0.2474 17103 91.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 158.02 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6401 0 4 0 6405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326527
X-RAY DIFFRACTIONf_angle_d0.64278857
X-RAY DIFFRACTIONf_chiral_restr0.04351032
X-RAY DIFFRACTIONf_plane_restr0.00421127
X-RAY DIFFRACTIONf_dihedral_angle_d11.91352409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.40.4311200.39551021X-RAY DIFFRACTION74.62
3.4-3.510.41681250.34271099X-RAY DIFFRACTION79.48
3.51-3.630.36281260.30411167X-RAY DIFFRACTION84.73
3.63-3.780.30041350.30451214X-RAY DIFFRACTION87.65
3.78-3.950.32951380.29171222X-RAY DIFFRACTION89.65
3.95-4.160.27811490.29461293X-RAY DIFFRACTION93.27
4.16-4.420.311490.24321348X-RAY DIFFRACTION96.39
4.42-4.760.23081490.21621352X-RAY DIFFRACTION97.47
4.76-5.240.2961540.24111381X-RAY DIFFRACTION98.33
5.24-5.990.29861550.27651390X-RAY DIFFRACTION98.72
6-7.540.31681550.27711415X-RAY DIFFRACTION98.74
7.55-49.330.20131670.18291479X-RAY DIFFRACTION99.46
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)
13.99985627702-2.415004158911.224770782932.9585310212-1.589414415088.64148384563-0.478954829352.844046090880.786133963585-0.8451593794630.0248895124447-0.107701167748-0.5011528798770.4739784456740.6146905671961.86104355456-0.4275210791910.1279964614260.7461454072890.1210385828161.2306779388629.75990020313.0942966013-1.08277693461
26.4048493286-4.04577200245-4.816010918357.504264103386.993224935086.74692409866-1.70794794363-2.00775927854-0.9143953000421.635971120872.783411758430.8369067033081.37054744622.050429147460.9584971218530.700835187009-0.5422873867840.5333389735970.344227492928-0.0914236692451.4050364737635.23654882168.768719876136.45372432063
36.541837025234.651076801441.853274223172.991477683161.144287647985.202242682460.3439368643910.0618054867801-0.09440407074460.118201733558-0.02192127366630.319215227886-0.0430659143720.15809370942-0.1799762263751.35695844650.09471991223010.1790775287130.541455765675-0.009221720658831.3633061233430.715326293310.90730422352.10558899261
42.03040714922-6.77845212547-4.049708860514.72271604364.802876326012.012711722-1.63905112036-0.571209787696-2.0792676491.9323404138-1.079581628710.93623067751-0.137811954201-2.726331026852.683465422390.7642266942290.06505168749630.005766111399150.725531794695-0.116846931981.4894917367220.1319622519.405902292920.160912722915
57.37346987252-1.17433796424-1.164068873750.5211524553840.2021405041254.02286816758-0.07099665235460.3678220241621.074756780180.5327088497570.2285468772331.02764428576-0.2604453254331.36695671109-0.2233143943891.20167186642-0.144562621651-0.02093562510530.552675110313-0.03462735349541.1024088142132.887433004811.17391355355.72195047886
67.470702755891.84306194486-0.8474756292244.50321949851.5501928678.41107632682-0.227313370076-0.2347201898820.8447962894070.3101808364160.160996220585-0.119151460872-0.8115824512050.118834741664-0.05704992000171.10377319515-0.00276481826308-0.05731362775420.691489406399-0.02668376008171.096904189819.2497636872222.411008488418.0435776056
76.179396657363.339775658830.29454007434.41332393788-2.35636985095.646214134461.25893053012-1.10190297298-2.01459373582-1.56903217822-2.47429510315-0.932580489911-0.579942212572-0.716139107087-0.0918844758361.36625799081-0.0215752621039-0.5132480951280.976254285185-0.2465431297121.290844589156.3375424365819.803143023115.4076279497
89.89890318661-3.22265119491-6.537951339952.848262473054.565751614889.61866775004-0.383478437605-2.092927108460.791877672939-1.878111187620.193989217604-1.282033875483.3657621938-0.611554984891-0.03329999455581.21030261691-0.223650455895-0.03879698318721.15591030465-0.0724847161421.1824771869812.179456839316.890428409122.5682026858
92.32240774137-0.2227163869920.549010906942.404013063391.494821121921.18764636864-1.3076431493-2.11576530163-1.341295154772.3163125314-1.673351553340.5606193114664.58781241968-0.948220876392.779872549711.95716111524-0.3221460839410.6012374380241.376975812940.01951013412081.3541308019810.04511138759.9292903871222.4435712015
103.51308072762-5.79509591355-2.390956908569.14467165574.347211952656.442890298871.321720350740.8175909963211.394316265370.0143813984045-0.755276468099-1.1036935935-1.57659055427-0.297181953018-0.4648677276521.7278684171-0.218504315849-0.03605664476210.7056787881970.01537723579731.103023014976.5606365830528.118056751711.0814878603
115.763934779964.62762713613-4.061275359888.8263462927-5.069840306916.97669956844-0.03346775100080.3228494120790.482203381104-0.931159607153-0.138719303676-0.3163093977070.09785507927340.2220929172630.3257358622291.53825850985-0.118339914490.08842502437310.724553009294-0.02022805517021.3755722794336.615154652232.5046285526-4.71686520553
128.29507486249-0.6673439868982.533870536234.60441781051-1.627575010483.140607042780.341153228253-0.766033349772-1.001246171080.185260443312-0.0215697391191-0.1622755785170.1708684314940.235527636857-0.2989746612451.14994600988-0.0222824602939-0.005556483926651.124892583850.03617778577541.0221148172844.24063553764.972281187527.7488655988
136.029803115120.879531560064-0.8045459699795.445686529384.08447251168.04100020883-0.199074157981-0.09095938242280.00183225675132-0.0867706716433-0.1227851411770.5213171419090.0209892222957-0.1520606340720.3706805392681.48606212479-0.15274210658-0.08374289899170.649845484893-0.1961522037651.2245444601419.475025774142.477274766825.9470406743
144.65276924121-2.23119533089-0.125641563656.4922829771-1.911364901391.77640849050.3269696803841.43103252624-0.0947869658986-0.6907263629150.05819252771410.4841060020370.355795261166-0.514110849895-0.4152426026591.209225633410.0457243148482-0.09480015015571.18835548027-0.0215215139290.814975794211-2.8988380812228.8042796553-6.46346553045
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 11 )AA-1 - 111 - 13
22chain 'A' and (resid 12 through 22 )AA12 - 2214 - 24
33chain 'A' and (resid 23 through 43 )AA23 - 4325 - 45
44chain 'A' and (resid 44 through 52 )AA44 - 5246 - 54
55chain 'A' and (resid 53 through 78 )AA53 - 7855 - 80
66chain 'B' and (resid -1 through 25 )BB-1 - 251 - 27
77chain 'B' and (resid 26 through 37 )BB26 - 3728 - 39
88chain 'B' and (resid 38 through 47 )BB38 - 4740 - 49
99chain 'B' and (resid 48 through 59 )BB48 - 5950 - 61
1010chain 'B' and (resid 60 through 78 )BB60 - 7862 - 80
1111chain 'C' and (resid 2 through 146 )CC2 - 1461 - 145
1212chain 'C' and (resid 147 through 335 )CC147 - 335146 - 328
1313chain 'D' and (resid 2 through 134 )DD2 - 1341 - 133
1414chain 'D' and (resid 135 through 335 )DD135 - 335134 - 329

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