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- PDB-8pps: Dimeric RbdA EAL, in apo state -

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Basic information

Entry
Database: PDB / ID: 8pps
TitleDimeric RbdA EAL, in apo state
ComponentsEAL domain-containing protein
KeywordsHYDROLASE / Phosphodiesterase / Dimeric / Magnesium bound
Function / homology
Function and homology information


regulation of single-species biofilm formation / cyclic-guanylate-specific phosphodiesterase activity / regulation of DNA-templated transcription / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain ...: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / EAL domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCordery, C.R. / Maly, M. / Walsh, M.A. / Tews, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
University of Southampton United Kingdom
CitationJournal: Rsc Chem Biol / Year: 2024
Title: Control of phosphodiesterase activity in the regulator of biofilm dispersal RbdA from Pseudomonas aeruginosa.
Authors: Cordery, C. / Craddock, J. / Maly, M. / Basavaraja, K. / Webb, J.S. / Walsh, M.A. / Tews, I.
History
DepositionJul 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EAL domain-containing protein
B: EAL domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,04914
Polymers60,2272
Non-polymers82212
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Checked with PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-27 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.400, 65.720, 172.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 546 - 797 / Label seq-ID: 18 - 269

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EAL domain-containing protein


Mass: 30113.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0861 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I580

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Non-polymers , 5 types, 200 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 61.8 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100mM Tris and BICINE pH 9 34% (w/v) ethylene glycol and PEG 8000 mix

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→46.04 Å / Num. obs: 31120 / % possible obs: 93.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 60.6 Å2 / CC1/2: 0.999 / CC star: 0.999 / Rrim(I) all: 0.059 / Net I/σ(I): 15.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.32 / Num. unique obs: 1890 / CC1/2: 0.665 / Rrim(I) all: 0.918 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XSCALEdata scaling
MOLREP11.7.03phasing
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.176 / SU B: 14.806 / SU ML: 0.171 / Average fsc free: 0.9548 / Average fsc work: 0.9692 / Cross valid method: FREE R-VALUE / ESU R: 0.254 / ESU R Free: 0.21
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2324 1495 4.804 %
Rwork0.1839 29625 -
all0.186 --
obs-31120 93.496 %
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: 58.816 Å2
Baniso -1Baniso -2Baniso -3
1-3.679 Å20 Å20 Å2
2---1.625 Å20 Å2
3----2.054 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 50 188 4195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124122
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163976
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.6525576
X-RAY DIFFRACTIONr_angle_other_deg0.5311.5669131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.405538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03610692
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.89910192
X-RAY DIFFRACTIONr_chiral_restr0.0740.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02954
X-RAY DIFFRACTIONr_nbd_refined0.2240.2841
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23533
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22019
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2152
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.28
X-RAY DIFFRACTIONr_nbd_other0.2370.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.211
X-RAY DIFFRACTIONr_mcbond_it4.194.2692025
X-RAY DIFFRACTIONr_mcbond_other4.194.2692025
X-RAY DIFFRACTIONr_mcangle_it6.1227.6612533
X-RAY DIFFRACTIONr_mcangle_other6.1217.6622534
X-RAY DIFFRACTIONr_scbond_it5.7764.8932097
X-RAY DIFFRACTIONr_scbond_other5.7754.8932098
X-RAY DIFFRACTIONr_scangle_it8.4788.6943043
X-RAY DIFFRACTIONr_scangle_other8.4778.6943044
X-RAY DIFFRACTIONr_lrange_it10.30742.0384527
X-RAY DIFFRACTIONr_lrange_other10.31741.8924506
X-RAY DIFFRACTIONr_ncsr_local_group_10.130.057613
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.129750.05008
12AX-RAY DIFFRACTIONLocal ncs0.129750.05008
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
2.3-2.360.304940.32218020.32124160.9010.90978.47680.301
2.36-2.4250.3031000.28919560.2923330.9280.93388.12690.264
2.425-2.4950.3091060.27121060.27323120.9250.94495.67470.24
2.495-2.5710.31040.23620540.23922240.9440.96197.03240.204
2.571-2.6550.27890.21319900.21521540.9540.9796.51810.178
2.655-2.7480.226830.17619370.17820930.9620.98196.51220.146
2.748-2.8510.276710.18718800.1920230.9660.97896.44090.154
2.851-2.9670.247810.17418320.17719730.9620.98296.95890.142
2.967-3.0990.236890.17117100.17418700.9640.98296.20320.147
3.099-3.2490.2681000.18316160.18817910.9590.97895.81240.161
3.249-3.4240.241890.17815540.18117250.9620.98295.24640.163
3.424-3.6310.215870.1814370.18216110.9760.98294.59960.168
3.631-3.8790.226620.17714040.17915450.9660.98494.88670.17
3.879-4.1880.217660.15112930.15414390.9730.98794.44060.149
4.188-4.5840.202740.15211700.15513360.9760.98693.11380.158
4.584-5.1180.278580.17110760.17612170.9580.98493.180.182
5.118-5.8980.239340.1899640.1910760.9690.98492.75090.199
5.898-7.1940.215390.1848200.1859360.9720.98191.77350.196
7.194-10.0520.133340.1446390.1437340.9890.98791.68940.17
10.052-46.040.228350.233850.234720.9660.96288.98310.284
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)
11.35890.23950.44541.04680.56981.4798-0.1054-0.0674-0.07530.0526-0.05550.00720.18710.00040.1610.05180.0410.03650.1836-0.01470.0477.1809-23.462-1.9846
21.85440.025-0.80172.1848-0.08671.9731-0.04640.0664-0.0615-0.0375-0.01340.0427-0.0209-0.06830.05970.19770.01580.09970.0060.00390.055824.5943-35.9842-40.9084
Refinement TLS groupSelection: ALL

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