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- PDB-9g86: Structure of Response regulator PleD in complex with c-diGMP and ... -

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Basic information

Entry
Database: PDB / ID: 9g86
TitleStructure of Response regulator PleD in complex with c-diGMP and pppGpp
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-0O2 / Chem-C2E / Response regulator PleD
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDugelay, C. / Jaboulay, 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 pppGpp
Authors: Dugelay, C. / Jaboulay, 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

Downloads & links

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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)206,59220
Polymers198,2394
Non-polymers8,35316
Water39622
1
A: Response regulator PleD
B: Response regulator PleD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,29610
Polymers99,1192
Non-polymers4,1778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Response regulator PleD
D: Response regulator PleD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,29610
Polymers99,1192
Non-polymers4,1778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.571, 132.571, 508.411
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)
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 11 or (resid 12...
d_2ens_1(chain "B" and (resid 2 through 11 or (resid 12...
d_3ens_1(chain "C" and (resid 2 through 66 or (resid 67...
d_4ens_1(chain "D" and (resid 2 through 11 or (resid 12...

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_11SERSERGLYGLYAA2 - 871 - 86
d_12GLYGLYALAALAAA89 - 14688 - 145
d_13ARGARGVALVALAA148 - 311147 - 310
d_14ARGARGLYSLYSAA313 - 452312 - 451
d_15C2EC2EC2EC2EAE501
d_21SERSERGLYGLYBB2 - 871 - 86
d_22GLYGLYVALVALBB89 - 31188 - 310
d_23ARGARGLYSLYSBB313 - 452312 - 451
d_24C2EC2EC2EC2EBJ503
d_31SERSERGLYGLYCC2 - 871 - 86
d_32GLYGLYALAALACC89 - 14688 - 145
d_33ARGARGVALVALCC148 - 311147 - 310
d_34ARGARGLYSLYSCC313 - 452312 - 451
d_35C2EC2EC2EC2ECM501
d_41SERSERGLYGLYDD2 - 871 - 86
d_42GLYGLYALAALADD89 - 14688 - 145
d_43ARGARGVALVALDD148 - 311147 - 310
d_44ARGARGLYSLYSDD313 - 452312 - 451
d_45C2EC2EC2EC2EDR503

NCS oper:
IDCodeMatrixVector
1given(-0.996218399245, -0.0297699160631, 0.0816250764423), (-0.026095691326, -0.793569452907, -0.607919845298), (0.0828728900234, -0.607750997952, 0.789791623524)71.9262064939, 3.6790953663, -2.10165612002
2given(-0.917216563242, 0.378455786003, 0.124438716465), (0.374667503867, 0.713268624551, 0.59234460475), (0.135418010841, 0.589931425907, -0.796016881145)73.6158277549, -53.6668526348, 107.795173614
3given(0.91220184769, -0.354581982588, -0.205327559512), (-0.346979949864, -0.9350140974, 0.0731679715195), (-0.217928207132, 0.00450058749347, -0.975954425805)9.36243366127, -25.2586625739, 121.444842995

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Components

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


Mass: 49559.691 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-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H18N5O20P5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl (Salt) 0.05 M Na Cacod 6.5 pH (Buffer) 10 %w/v PEG 4K (Precipitant) 0.5 mM Spermine (Additive)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980114 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980114 Å / Relative weight: 1
ReflectionResolution: 3→48.96 Å / Num. obs: 54311 / % possible obs: 100 % / Redundancy: 33.6 % / Biso Wilson estimate: 71.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.361 / Rpim(I) all: 0.062 / Rrim(I) all: 0.366 / Χ2: 1.01 / Net I/σ(I): 12.6 / Num. measured all: 1825849
Reflection shellResolution: 3→3.09 Å / % possible obs: 100 % / Redundancy: 32.4 % / Rmerge(I) obs: 3.305 / Num. measured all: 141102 / Num. unique obs: 4359 / CC1/2: 0.47 / Rpim(I) all: 0.58 / Rrim(I) all: 3.356 / Χ2: 0.97 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.53 Å / SU ML: 0.3671 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2789 5.15 %Random selection
Rwork0.1897 51373 --
obs0.1917 54162 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.79 Å2
Refinement stepCycle: LAST / Resolution: 3→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13572 0 532 22 14126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004314324
X-RAY DIFFRACTIONf_angle_d0.868719529
X-RAY DIFFRACTIONf_chiral_restr0.04922280
X-RAY DIFFRACTIONf_plane_restr0.01962485
X-RAY DIFFRACTIONf_dihedral_angle_d18.52085341
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.868111777533
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.19776848682
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.26381153844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.35441400.33122488X-RAY DIFFRACTION99.96
3.05-3.110.38791370.32062514X-RAY DIFFRACTION100
3.11-3.170.35421480.29392515X-RAY DIFFRACTION100
3.17-3.230.25371290.27282532X-RAY DIFFRACTION100
3.23-3.30.29051470.25882503X-RAY DIFFRACTION100
3.3-3.380.32431410.24372493X-RAY DIFFRACTION100
3.38-3.460.2441330.22392510X-RAY DIFFRACTION100
3.46-3.560.25931380.2142538X-RAY DIFFRACTION100
3.56-3.660.26561410.21122524X-RAY DIFFRACTION100
3.66-3.780.23961450.20072544X-RAY DIFFRACTION100
3.78-3.910.22131150.18442563X-RAY DIFFRACTION100
3.91-4.070.25481410.18122540X-RAY DIFFRACTION100
4.07-4.260.19391280.17742576X-RAY DIFFRACTION100
4.26-4.480.20651470.16122547X-RAY DIFFRACTION100
4.48-4.760.19511450.1472572X-RAY DIFFRACTION100
4.76-5.130.21481540.14912587X-RAY DIFFRACTION99.96
5.13-5.640.18371340.16242597X-RAY DIFFRACTION100
5.64-6.460.22731420.18762641X-RAY DIFFRACTION100
6.46-8.130.18281430.1692691X-RAY DIFFRACTION100
8.13-47.530.18431410.16322898X-RAY DIFFRACTION99.61
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)
11.95511398678-0.537489642333-0.1621244824251.345509939470.4554297137622.020925381350.07030144500280.06867408146180.0340020162238-0.0282891635811-0.0118139013447-0.0908411682068-0.2139874085220.05695166365050.0205032702890.531779940848-0.00954081589421-0.05046195663750.331900843025-0.002478942144370.41111912754527.9992107937-18.028659661914.7663757877
21.339061590340.307235682619-0.2608224037761.18000035438-0.5733287676792.46560514906-0.0123802132786-0.1506819752270.0481498430269-0.285423736898-0.2435734793840.149725784123-0.07910171000850.3758491220450.04175459193390.6264945729730.00576453951845-0.07236349275820.5426714161570.01035360891530.62076967746860.4829403045-11.275537299847.0042701636
32.7568623721-0.3710444135690.4123196751831.12108058503-0.0691931181711.6311479778-0.0821310047676-0.05703306337010.543693251826-0.003367044470220.007112588021310.0712290747643-0.1542555435830.1526814865730.144031455930.835630550713-0.125439067086-0.03238486068820.4936184809560.01903032440640.6976004123345.78223623658.3082636701922.4928932957
41.447279151640.06042622764620.5827379463561.12042053571-0.1293776505353.266350509710.0249130498245-0.2346322102220.04326600653230.0837114011534-0.0868424927918-0.159845151121-0.350167353187-0.5483048870650.02799422939350.6447498739420.0450873064864-0.01248700594730.571328231676-0.1278047050270.47608607032915.9519853453-17.657238757147.1021110929
52.505458749020.32510790523-0.3331279792052.60434985918-0.03313412624181.10739686354-0.00513317702902-0.0477889056471-0.2114605256830.003542487330580.01608207548960.1913827274110.009608827791010.06551076889550.05844297876520.5212360119160.1375129365610.01553211639790.4761377211610.0206951117070.46047715981842.9717590365-47.033399338689.1479748614
61.63548464052-0.7860068089130.2851693916341.86422156003-0.2637344326982.54563850669-0.1138038117160.0860958889889-0.0412466635295-0.06771380135470.05504424671110.042674851363-0.287764580432-0.2413468851390.01302215533470.6008252434330.0121026508642-0.09242591967190.571270124342-0.1139818996820.5239653553419.6087115112-11.631623819171.9385729763
71.954291569070.2621978378250.2093543586562.400302864260.2405565966151.45497433547-0.128504841722-0.232750600172-0.04698266740790.282106927790.168980262729-0.1470398414310.02767831401040.03188016066960.0381798831320.5532571518380.1249284937840.005955328227670.520460880415-0.07850363997170.39894981273738.4604063422-17.1865676089100.875823021
81.45769577969-0.417579917978-0.1416952844812.44341326363-1.053494379062.89561005480.04432749527730.02689248095840.141403980533-0.171780299048-0.330272167154-0.0388367924190.220530943110.4790746346930.0660882484880.5259803188110.01770671391310.0703975243950.5709811450040.03093381141590.67112634257758.8302944369-31.894420581562.4547371671
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 280 )AA2 - 2801 - 274
22chain 'A' and (resid 281 through 454 )AA281 - 454275 - 448
33chain 'B' and (resid 2 through 280 )BE2 - 2801 - 273
44chain 'B' and (resid 281 through 452 )BE281 - 452274 - 445
55chain 'C' and (resid 2 through 280 )CI2 - 2801 - 274
66chain 'C' and (resid 281 through 454 )CI281 - 454275 - 448
77chain 'D' and (resid 2 through 280 )DM2 - 2801 - 274
88chain 'D' and (resid 281 through 454 )DM281 - 454275 - 448

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