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- PDB-4rnj: PaMorA phosphodiesterase domain, apo form -

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Basic information

Entry
Database: PDB / ID: 4rnj
TitlePaMorA phosphodiesterase domain, apo form
ComponentsMotility regulator
KeywordsHYDROLASE / EAL domain / Phosphodiesterase / c-di-GMP
Function / homology
Function and homology information


nucleotide binding / regulation of DNA-templated transcription / identical protein binding / membrane / metal ion binding
Similarity search - Function
: / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / PAS fold-3 / EAL domain / PAS fold / Diguanylate cyclase, GGDEF domain ...: / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / PAS fold-3 / EAL domain / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Motility regulator
B: Motility regulator


Theoretical massNumber of molelcules
Total (without water)63,4552
Polymers63,4552
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Motility regulator


Theoretical massNumber of molelcules
Total (without water)31,7271
Polymers31,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Motility regulator


Theoretical massNumber of molelcules
Total (without water)31,7271
Polymers31,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.071, 79.895, 138.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsActive diguanylate cyclase

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Components

#1: Protein Motility regulator


Mass: 31727.320 Da / Num. of mol.: 2 / Fragment: EAL domain, UNP residues 1145-1409
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, cyclic-guanylate-specific phosphodiesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Imidazole; MES, 0.09M NaN03; Na2HPO4; (NH4)2SO4, 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: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 14, 2012
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.32→100 Å / Num. all: 25794 / Num. obs: 25720 / % possible obs: 99.7 % / Redundancy: 4.28 % / Biso Wilson estimate: 42.67 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.87
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N3T

3n3t


Resolution: 2.32→48.741 Å / FOM work R set: 0.8062 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1310 5.09 %RANDOM
Rwork0.1968 ---
obs0.1997 25717 99.71 %-
all-25794 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.79 Å2 / Biso mean: 47.68 Å2 / Biso min: 25.23 Å2
Refinement stepCycle: LAST / Resolution: 2.32→48.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 0 117 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134056
X-RAY DIFFRACTIONf_angle_d1.4315488
X-RAY DIFFRACTIONf_chiral_restr0.084612
X-RAY DIFFRACTIONf_plane_restr0.007720
X-RAY DIFFRACTIONf_dihedral_angle_d15.1461519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.41290.33351300.28462650278099
2.4129-2.52270.31961430.263626762819100
2.5227-2.65570.29711650.238526672832100
2.6557-2.82210.27931300.232626802810100
2.8221-3.03990.30551580.228626662824100
3.0399-3.34580.28921280.222527242852100
3.3458-3.82980.26271600.198627092869100
3.8298-4.82440.1951550.157627442899100
4.8244-48.75160.22141410.165928913032100

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