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- PDB-5mf5: PA3825-EAL Mg-CdG Structure -

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Basic information

Entry
Database: PDB / ID: 5mf5
TitlePA3825-EAL Mg-CdG Structure
ComponentsDiguanylate phosphodiesterase
KeywordsHYDROLASE / EAL / Phosphodiesterase / biofilm formation / P Aeruginosa / PA3825
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Putative cyclic diguanylate phosphodiesterase, CSS motif-containing domain / CSS motif domain associated with EAL / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / : / cyclic-guanylate-specific phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsHorrell, S. / Bellini, D. / Strange, R. / Wagner, A. / Walsh, M.
CitationJournal: Sci Rep / Year: 2017
Title: Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases.
Authors: Bellini, D. / Horrell, S. / Hutchin, A. / Phippen, C.W. / Strange, R.W. / Cai, Y. / Wagner, A. / Webb, J.S. / Tews, I. / Walsh, M.A.
History
DepositionNov 17, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionDec 21, 2016ID: 4Y9Q
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Jul 3, 2019Group: Advisory / Data collection / Source and taxonomy
Category: database_PDB_remark / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _database_PDB_remark.text / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diguanylate phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2455
Polymers28,4821
Non-polymers7634
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-25 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.590, 64.590, 135.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-451-

HOH

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Components

#1: Protein Diguanylate phosphodiesterase


Mass: 28481.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AO964_02925 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: A0A140SMD7, UniProt: Q9HXH7*PLUS
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic and 0.1 M sodium acetate pH 4.5, 0.2 M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→29.16 Å / Num. obs: 28763 / % possible obs: 99.6 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 18.8 / Num. measured all: 178724
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.77-1.826.70.651379020720.8510.2670.7052.699.9
7.92-29.165.30.019211239810.0080.02155.798.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.3.6data scaling
PDB_EXTRACT3.2data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y9O

4y9o


Resolution: 1.77→29.16 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.02 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1427 5 %RANDOM
Rwork0.1977 ---
obs0.1994 27262 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.43 Å2 / Biso mean: 32.941 Å2 / Biso min: 14.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å2-0 Å2
2--1.08 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: final / Resolution: 1.77→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 49 168 2221
Biso mean--24.41 37.32 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192182
X-RAY DIFFRACTIONr_bond_other_d0.0070.022069
X-RAY DIFFRACTIONr_angle_refined_deg1.6372.0132964
X-RAY DIFFRACTIONr_angle_other_deg1.00134753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71822.95998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6591521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212452
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02495
X-RAY DIFFRACTIONr_mcbond_it2.3723.0931062
X-RAY DIFFRACTIONr_mcbond_other2.3723.091061
X-RAY DIFFRACTIONr_mcangle_it3.5114.6141338
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 119 -
Rwork0.287 1940 -
all-2059 -
obs--99.81 %

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