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- PDB-4rni: PaMorA dimeric phosphodiesterase. apo form -

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Basic information

Entry
Database: PDB / ID: 4rni
TitlePaMorA dimeric phosphodiesterase. apo form
ComponentsMotility regulator
KeywordsHYDROLASE / EAL domain / Phosphodiesterase / 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 / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Nucleotide cyclase / 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 / molecular replacement / Resolution: 2.17 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

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
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-12 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.754, 94.466, 154.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
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 / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M magnesium chloride, 0.1M Bis Tris, 25% PEG 3350 , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Details: fixed monochromator 22m
RadiationMonochromator: fixed monochromator 22m / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.17→80.62 Å / Num. all: 28887 / Num. obs: 28802 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 36.95 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.3
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2106 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.594
Highest resolutionLowest resolution
Rotation29.4 Å2.39 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→80.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2166 / WRfactor Rwork: 0.1665 / FOM work R set: 0.8294 / SU B: 5.819 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2581 / SU Rfree: 0.2081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 2000 6.9 %RANDOM
Rwork0.1812 ---
obs0.1851 28802 99.7 %-
all-28887 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.77 Å2 / Biso mean: 36.872 Å2 / Biso min: 15.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--1.67 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.17→80.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 0 206 4167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194039
X-RAY DIFFRACTIONr_bond_other_d0.0020.023934
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9795466
X-RAY DIFFRACTIONr_angle_other_deg0.8639029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23323.757189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4415698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1971534
X-RAY DIFFRACTIONr_chiral_restr0.0970.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_mcbond_it3.1913.292026
X-RAY DIFFRACTIONr_mcbond_other3.1853.2872025
X-RAY DIFFRACTIONr_mcangle_it4.4944.9172529
LS refinement shellResolution: 2.166→2.222 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 142 -
Rwork0.25 1899 -
all-2041 -
obs--96.82 %

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