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- PDB-9g85: Structure of Response regulator PleD in complex with c-diGMP and ppGpp -

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Basic information

Entry
Database: PDB / ID: 9g85
TitleStructure of Response regulator PleD in complex with c-diGMP and ppGpp
ComponentsResponse regulator PleD
KeywordsSIGNALING PROTEIN / inhibitor complex
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / phosphorelay signal transduction system / cell differentiation / GTP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Chem-C2E / GUANOSINE-5',3'-TETRAPHOSPHATE / Response regulator PleD
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsJaboulay, C. / Dugelay, C. / Guzzo, M. / Terradot, L.
Funding support France, 1items
OrganizationGrant numberCountry
ATIP-Avenir France
CitationJournal: To Be Published
Title: Structure of Response regulator PleD in complex with c-diGMP and ppGpp
Authors: Jaboulay, C. / Dugelay, C. / Guzzo, M. / Terradot, L.
History
DepositionJul 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator PleD
B: Response regulator PleD
C: Response regulator PleD
D: Response regulator PleD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,89424
Polymers198,7644
Non-polymers8,13020
Water61334
1
A: Response regulator PleD
C: Response regulator PleD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,44712
Polymers99,3822
Non-polymers4,06510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Response regulator PleD
D: Response regulator PleD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,44712
Polymers99,3822
Non-polymers4,06510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.001, 133.001, 510.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11D-609-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 87 or (resid 88...
d_2ens_1(chain "B" and (resid 3 through 135 or resid 148...
d_3ens_1(chain "C" and (resid 3 through 87 or (resid 88...
d_4ens_1(chain "D" and (resid 3 through 87 or (resid 88...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALASERSERAA3 - 1353 - 135
d_12ARGARGGLYGLYAA148 - 451148 - 451
d_13C2EC2EC2EC2EAE501
d_14C2EC2EC2EC2ECP502
d_15G4PG4PG4PG4PAF502
d_21ALAALASERSERBB3 - 1353 - 135
d_22ARGARGGLYGLYBB148 - 451148 - 451
d_23C2EC2EC2EC2EBI501
d_24C2EC2EC2EC2EBJ502
d_25G4PG4PG4PG4PBK503
d_31ALAALASERSERCC3 - 1353 - 135
d_32ARGARGGLYGLYCC148 - 451148 - 451
d_33C2EC2EC2EC2ECQ503
d_34C2EC2EC2EC2ECR504
d_35G4PG4PG4PG4PCS505
d_41ALAALASERSERDD3 - 1353 - 135
d_42ARGARGGLYGLYDD148 - 451148 - 451
d_43C2EC2EC2EC2EBL504
d_44C2EC2EC2EC2EDV502
d_45G4PG4PG4PG4PDW503

NCS oper:
IDCodeMatrixVector
1given(-0.164573844163, -0.973836921065, -0.156707054683), (-0.971778515261, 0.132859583806, 0.194922672535), (-0.169002861203, 0.184363722465, -0.9682190097)153.622601238, 93.6006319548, 234.318467789
2given(-0.779312967256, 0.0749716793322, 0.62213386531), (0.0927042971357, -0.968098854106, 0.232788577838), (0.619739632717, 0.239089640046, 0.747501793752)101.731331187, 10.9754746786, -37.4438708928
3given(-0.0390665538629, 0.895567978327, -0.443206273157), (0.891521074234, -0.169081827317, -0.420239824228), (-0.45129145634, -0.411545054481, -0.791812281773)130.580990818, -11.7711502623, 255.910152221

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Components

#1: Protein
Response regulator PleD / Stalked cell differentiation-controlling protein


Mass: 49690.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: pleD, CC_2462 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5I5, diguanylate cyclase
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M KCl (Salt) 0.01 M MgCl2 (Salt) 0.05 M MES 5.6 pH (Buffer) 5 %w/v PEG 8K (Precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.9→47.7 Å / Num. obs: 60601 / % possible obs: 100 % / Redundancy: 38.8 % / Biso Wilson estimate: 76.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.426 / Rpim(I) all: 0.069 / Rrim(I) all: 0.432 / Χ2: 1.01 / Net I/σ(I): 11.3 / Num. measured all: 2352269
Reflection shellResolution: 2.9→2.98 Å / % possible obs: 100 % / Redundancy: 40.1 % / Rmerge(I) obs: 4.999 / Num. measured all: 175010 / Num. unique obs: 4360 / CC1/2: 0.608 / Rpim(I) all: 0.793 / Rrim(I) all: 5.063 / Χ2: 0.98 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.7 Å / SU ML: 0.4442 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 3013 4.99 %
Rwork0.2009 57417 -
obs0.2028 60430 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.13 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13500 0 520 34 14054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003114235
X-RAY DIFFRACTIONf_angle_d0.818219405
X-RAY DIFFRACTIONf_chiral_restr0.05422269
X-RAY DIFFRACTIONf_plane_restr0.00632474
X-RAY DIFFRACTIONf_dihedral_angle_d17.1175327
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.811103770503
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.816969649204
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.86186532115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.950.45371430.39792543X-RAY DIFFRACTION99.93
2.95-2.990.44241210.37542548X-RAY DIFFRACTION100
2.99-3.050.40341310.3312565X-RAY DIFFRACTION99.93
3.05-3.10.35371360.30592565X-RAY DIFFRACTION99.93
3.1-3.160.3681240.26962559X-RAY DIFFRACTION99.93
3.16-3.220.28791230.2632565X-RAY DIFFRACTION99.93
3.22-3.290.33081410.26132562X-RAY DIFFRACTION99.78
3.29-3.370.29751470.25942551X-RAY DIFFRACTION99.96
3.37-3.460.30071470.2542539X-RAY DIFFRACTION99.85
3.46-3.550.33881250.25172603X-RAY DIFFRACTION99.89
3.55-3.650.24411400.21192554X-RAY DIFFRACTION100
3.65-3.770.25031420.19152581X-RAY DIFFRACTION99.93
3.77-3.910.21071550.18062592X-RAY DIFFRACTION99.85
3.91-4.060.22051260.17762588X-RAY DIFFRACTION99.96
4.06-4.250.21531610.17352582X-RAY DIFFRACTION99.85
4.25-4.470.21360.16492611X-RAY DIFFRACTION99.82
4.47-4.750.19171330.14872641X-RAY DIFFRACTION99.96
4.75-5.120.17961320.15952645X-RAY DIFFRACTION99.96
5.12-5.630.21131240.17642652X-RAY DIFFRACTION99.89
5.63-6.440.22911530.2112668X-RAY DIFFRACTION100
6.45-8.110.20351290.19972755X-RAY DIFFRACTION99.97
8.11-47.70.19841440.16852948X-RAY DIFFRACTION99.71
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)
11.877031515540.850605140008-0.5130976482173.611365567180.6782739627311.6079111935-0.0195065318141-0.0416568504243-0.0230633075658-0.04636818520890.08187928665270.08963546576120.0478163847591-0.0355885839327-0.05714423637470.4400144762960.0295933938333-0.005559590223480.6599115193130.01892760866330.4883107211469.903387934412.618983827180.6025453848
22.224252427220.2229055023580.7209099263252.321680385670.4738549076683.715218801470.0562278273071-0.16954142479-0.1245973269540.0788782638620.009008623890020.005861074424760.02187103003310.147880565587-0.03789556543880.5907583138260.01973155601690.06217917430020.6333925012890.0765342802930.541278115984113.11808437710.103282364397.4196746545
33.48110429222-1.36693203020.7706829211711.35991881929-0.1873579771751.63424632951-0.0592115407450.1806377539210.388729283452-0.003850813965-0.0483826139814-0.235182785091-0.2339261259950.225571643120.09740120200470.678644670017-0.300072671549-0.04737040401780.7510429704540.05852562903160.450600937258117.29017757343.3761999214147.395868977
41.1753449627-0.372934109196-0.3275366437032.06282241104-0.1591745743663.89196197199-0.05068333786460.2207202639210.115281727514-0.2540319446830.0437478010646-0.06429355632580.3062255154580.626186722398-0.01579421579030.499804451832-0.02093132959080.05891398577380.7897676123920.1100413737660.460939487367109.3744517233.74523809031123.325961618
51.98189939645-0.1137812041120.4365023428512.78503094289-0.5149250215841.076281968370.03741665456010.5108920693270.173503092261-0.285571607689-0.002225122063490.006198459294470.027595866199-0.0583460772974-0.03259361206740.5315853291290.02228653103370.05302742453310.7418920636440.04207321633220.44744601874798.268961320123.677953178468.3565483441
62.98807763424-0.05512278001470.6340550405660.7083197773740.07850721491333.047220261380.0455472859522-0.381223974774-0.127680184960.133719189831-0.2066364013840.0967729741843-0.224394365952-0.3317449713180.1301835006690.661521687082-0.07468670956070.009910424515040.662056546956-0.0919749044280.75366680763575.397345671933.9778334986107.933971477
72.655930693180.919801405854-0.5937115918973.653759533360.7859084909893.454353510460.0719238322146-0.435270639685-0.1216149632570.1717885207440.1363118516260.236404278877-0.1544263705460.161441677764-0.170463916650.49350087768-0.0315386755320.01888062960790.6395214540120.07454429196710.5185089190392.063221435814.9274748484164.006034997
82.41784515924-0.225968151598-0.9497712788383.142902588990.2732519515242.47421355466-0.1009530498710.0952294336430.260531233403-0.0960964769960.0893093040769-0.246302654711-0.1433126755380.5836171484090.01144748836680.445196157249-0.118940353397-0.02698494192940.6726725552170.08332032654510.404452890231110.6549681813.9313443231150.487076384
91.46625767853-0.02082900448380.5754300356982.185455527861.348260791174.17074108355-0.0375475204872-0.158860662469-0.0120905497777-0.0139723834407-0.2107261044470.0152575530019-0.302752499925-0.07273454097530.2469548479450.686911744418-0.098955478499-0.05676480222830.6901904177850.1175034260590.71837153358892.257012855146.4625390952123.474775203
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 282 )AA3 - 2821 - 275
22chain 'A' and (resid 283 through 454 )AA283 - 454276 - 447
33chain 'B' and (resid 3 through 280 )BF3 - 2801 - 270
44chain 'B' and (resid 281 through 451 )BF - J281 - 451271
55chain 'C' and (resid 3 through 280 )CK3 - 2801 - 267
66chain 'C' and (resid 281 through 452 )CK281 - 452268 - 439
77chain 'D' and (resid 2 through 108 )DO2 - 1081 - 107
88chain 'D' and (resid 109 through 280 )DO109 - 280108 - 274
99chain 'D' and (resid 281 through 453 )DO281 - 453275 - 447

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