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- PDB-9t28: WspR response regulator with crystallization epitope mutations G3... -

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Basic information

Entry
Database: PDB / ID: 9t28
TitleWspR response regulator with crystallization epitope mutations G306D:G308D
Componentsdiguanylate cyclase
KeywordsSIGNALING PROTEIN / crystal epitopes
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 / nucleotide binding / metal ion binding / identical protein binding / plasma membrane
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsFairhead, M. / Wiggers, H. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. ...Fairhead, M. / Wiggers, H. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: WspR response regulator with crystallization epitope mutations G306D:G308D
Authors: Fairhead, M. / Wiggers, H. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / ...Authors: Fairhead, M. / Wiggers, H. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionOct 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 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: diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7182
Polymers18,6221
Non-polymers961
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.12, 45.4, 85.23
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein diguanylate cyclase


Mass: 18621.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: wspR, PA3702 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXT9, diguanylate cyclase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.77 Å3/Da / Density % sol: 30.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate 25% PEG3350 0.1M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91739 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91739 Å / Relative weight: 1
ReflectionResolution: 1.2→42.615 Å / Num. obs: 37725 / % possible obs: 89.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 20.5
Reflection shellResolution: 1.2→1.23 Å / Num. unique obs: 1400 / Rrim(I) all: 0.829

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→42.615 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.371 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2133 1504 4.891 %
Rwork0.1639 29247 -
all0.166 --
obs-30751 98.605 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0 Å2
2---0.035 Å20 Å2
3---0.445 Å2
Refinement stepCycle: LAST / Resolution: 1.33→42.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 5 74 1383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121412
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161302
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.821918
X-RAY DIFFRACTIONr_angle_other_deg0.7711.7622983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.751515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55810239
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4531072
X-RAY DIFFRACTIONr_chiral_restr0.0980.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021789
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02357
X-RAY DIFFRACTIONr_nbd_refined0.2340.2295
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21191
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2722
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1570.223
X-RAY DIFFRACTIONr_nbd_other0.1940.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.211
X-RAY DIFFRACTIONr_mcbond_it4.6611.535716
X-RAY DIFFRACTIONr_mcbond_other4.6281.536716
X-RAY DIFFRACTIONr_mcangle_it6.5432.761909
X-RAY DIFFRACTIONr_mcangle_other6.5492.764910
X-RAY DIFFRACTIONr_scbond_it7.0191.926696
X-RAY DIFFRACTIONr_scbond_other7.0151.934693
X-RAY DIFFRACTIONr_scangle_it9.8863.3731009
X-RAY DIFFRACTIONr_scangle_other9.8863.3821004
X-RAY DIFFRACTIONr_lrange_it13.30919.3581649
X-RAY DIFFRACTIONr_lrange_other12.93119.1271636
X-RAY DIFFRACTIONr_rigid_bond_restr3.77832714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.33-1.3650.2931040.26919780.2722640.9370.95591.96110.254
1.365-1.4020.2521170.22320580.22421940.960.97199.1340.2
1.402-1.4420.2311120.19820020.221480.9640.97698.41710.174
1.442-1.4870.2421240.16519640.16921010.9580.98399.38120.139
1.487-1.5360.2121040.14419180.14820390.9710.98799.16630.122
1.536-1.5890.236880.13818260.14319350.9640.98898.91470.117
1.589-1.6490.21910.1318060.13419060.9740.98999.52780.111
1.649-1.7160.228870.13217280.13618440.9670.98998.42730.115
1.716-1.7930.223800.13116750.13517590.9640.98999.77260.116
1.793-1.880.193680.13916130.14116850.9760.98899.76260.125
1.88-1.9810.204780.14415340.14716210.9720.98899.44480.131
1.981-2.1010.187810.14814370.1515210.9790.98799.80280.139
2.101-2.2460.198750.15413470.15714370.9740.98698.95620.149
2.246-2.4250.191590.15712710.15813580.980.98497.93810.152
2.425-2.6560.211580.16511710.16712320.9720.98399.75650.168
2.656-2.9680.235520.17210830.17511350.9680.9811000.178
2.968-3.4250.176380.1779830.17710250.9810.9899.60980.188
3.425-4.1880.213380.1658100.1688620.9720.98398.37590.182
4.188-5.8940.221300.1886380.1896920.9730.98396.53180.217
5.894-42.6150.268200.1874050.194280.9370.96899.29910.219

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