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- PDB-4rnf: PaMorA tandem diguanylate cyclase - mutant phosphodiesterase, apo form -

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Basic information

Entry
Database: PDB / ID: 4rnf
TitlePaMorA tandem diguanylate cyclase - mutant phosphodiesterase, apo form
ComponentsMotility regulator
KeywordsTransferase / Hydrolase / Tandem GGDEF and EAL domain / Diguanylate cyclase / Phosphodiesterase / GTP / c-di-GMP
Function / homology
Function and homology information


nucleotide binding / regulation of DNA-templated transcription / membrane / identical protein binding / metal ion binding
Similarity search - Function
EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase ...EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAS domain / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Nucleotide cyclase / PAS fold / PAS fold / Reverse transcriptase/Diguanylate cyclase domain / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPhippen, C.W. / Tews, I.
CitationJournal: Febs Lett. / Year: 2014
Title: Formation and dimerization of the phosphodiesterase active site of the Pseudomonas aeruginosa MorA, a bi-functional c-di-GMP regulator.
Authors: Phippen, C.W. / Mikolajek, H. / Schlaefli, H.G. / Keevil, C.W. / Webb, J.S. / Tews, I.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Motility regulator


Theoretical massNumber of molelcules
Total (without water)50,4461
Polymers50,4461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.744, 47.352, 60.010
Angle α, β, γ (deg.)82.15, 71.63, 70.66
Int Tables number1
Space group name H-MP1
DetailsActive diguanylate cyclase and Active phosphodiesterase are dimers.

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Components

#1: Protein Motility regulator


Mass: 50445.535 Da / Num. of mol.: 1 / Fragment: GGDEF domain, EAL domain, UNP residues 978-1409 / Mutation: D1310N, D1311N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PA01 / Gene: morA, PA4601 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9HVI8, diguanylate cyclase, cyclic-guanylate-specific phosphodiesterase

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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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 295 K / pH: 6.5
Details: 0.1M Imidazole; MES, 0.12M 1,6-Hexanediol; 1-Butanol 1,2-Propanediol (racemic); 2-Propanol; 1,4-Butanediol; 1,3-Propanediol, 30% Ethylene glycol; PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR 28.290M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.85→28.46 Å / Num. obs: 9235 / % possible obs: 98.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 36.34 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 7.4
Reflection shellResolution: 2.85→3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.4 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→28.46 Å / SU ML: 0.35 / σ(F): 1.97 / Phase error: 30.86 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflection
Rfree0.278 440 4.77 %
Rwork0.239 --
obs0.241 9225 98.5 %
all-9377 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 2.85→28.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 0 0 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143371
X-RAY DIFFRACTIONf_angle_d1.374558
X-RAY DIFFRACTIONf_dihedral_angle_d16.4521252
X-RAY DIFFRACTIONf_chiral_restr0.108508
X-RAY DIFFRACTIONf_plane_restr0.006601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-3.2620.35991490.30372898X-RAY DIFFRACTION98
3.262-4.10780.28221400.2412948X-RAY DIFFRACTION98
4.1078-28.45940.23911510.20732939X-RAY DIFFRACTION99

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