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- PDB-5m3c: Structure of the hybrid domain (GGDEF-EAL) of PA0575 from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 5m3c
TitleStructure of the hybrid domain (GGDEF-EAL) of PA0575 from Pseudomonas aeruginosa PAO1 at 2.8 Ang. with GTP and Ca2+ bound to the active site of the GGDEF domain
ComponentsDiguanylate cyclase
KeywordsHYDROLASE / phosphodiesterase / c-di-GMP / cyclic-di-GMP / diguanylate / cyclase / EAL / GGDEF
Function / homology
Function and homology information


membrane => GO:0016020
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 / Bacterial periplasmic substrate-binding proteins / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Nucleotide cyclase / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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
GUANOSINE-5'-TRIPHOSPHATE / : / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsGiardina, G. / Brunotti, P. / Cutruzzola, F. / Rinaldo, S.
Funding support Italy, 3items
OrganizationGrant numberCountry
Pasteur Institute- Cenci Bolognetti FoundationFunds 2015-17 to Francesca Cutruzzola' Italy
MIURRBFR10LHD1 Italy
Sapienza University of RomeB52I15003420005 Italy
CitationJournal: FEBS J. / Year: 2018
Title: Insights into the GTP-dependent allosteric control of c-di-GMP hydrolysis from the crystal structure of PA0575 protein from Pseudomonas aeruginosa.
Authors: Mantoni, F. / Paiardini, A. / Brunotti, P. / D'Angelo, C. / Cervoni, L. / Paone, A. / Cappellacci, L. / Petrelli, R. / Ricciutelli, M. / Leoni, L. / Rampioni, G. / Arcovito, A. / Rinaldo, S. ...Authors: Mantoni, F. / Paiardini, A. / Brunotti, P. / D'Angelo, C. / Cervoni, L. / Paone, A. / Cappellacci, L. / Petrelli, R. / Ricciutelli, M. / Leoni, L. / Rampioni, G. / Arcovito, A. / Rinaldo, S. / Cutruzzola, F. / Giardina, G.
History
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diguanylate cyclase
B: Diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4129
Polymers98,1662
Non-polymers1,2477
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-82 kcal/mol
Surface area36000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.307, 133.931, 69.141
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Diguanylate cyclase


Mass: 49082.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AO964_16615 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A140SCF9, UniProt: Q9I5W1*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 3 mg/ml in 20 mM Tris pH 7.6, 150 mM, CaCl2 2,5mM, GTP 0.32 mM mixing volumes 1 microL (1:1) Reservoir: PEG 4K 2%, CaCl2 0,01M, KCl 0,05 M, sodium cacodilato pH 6 0,05M ...Details: Protein solution: 3 mg/ml in 20 mM Tris pH 7.6, 150 mM, CaCl2 2,5mM, GTP 0.32 mM mixing volumes 1 microL (1:1) Reservoir: PEG 4K 2%, CaCl2 0,01M, KCl 0,05 M, sodium cacodilato pH 6 0,05M Cryo-protection:PEG 4K raised to 3%, addition of 20% glycerol
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.894 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Jun 23, 2016
RadiationMonochromator: KMC-3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.894 Å / Relative weight: 1
ReflectionResolution: 2.8→48.1 Å / Num. obs: 28700 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 55.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.8-2.958.41.3420.74199.7
8.85-48.15.20.030.998198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.13 Å48.1 Å
Translation5.13 Å48.1 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RNJ, 4IOB

4rnj

4iob


Resolution: 2.8→48.1 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.896 / SU B: 19.254 / SU ML: 0.354 / SU R Cruickshank DPI: 1.5643 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.563 / ESU R Free: 0.386
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 1388 4.8 %RANDOM
Rwork0.2436 ---
obs0.2452 27257 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.57 Å2 / Biso mean: 61.268 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--4.84 Å20 Å20 Å2
2--2.6 Å20 Å2
3---2.24 Å2
Refinement stepCycle: final / Resolution: 2.8→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 0 69 15 6495
Biso mean--57.88 42.92 -
Num. residues----846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0196611
X-RAY DIFFRACTIONr_bond_other_d00.026202
X-RAY DIFFRACTIONr_angle_refined_deg0.7411.9968996
X-RAY DIFFRACTIONr_angle_other_deg0.543314239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9965843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06624.246285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1281541
X-RAY DIFFRACTIONr_chiral_restr0.040.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217502
X-RAY DIFFRACTIONr_gen_planes_other00.021447
X-RAY DIFFRACTIONr_mcbond_it1.2266.3453381
X-RAY DIFFRACTIONr_mcbond_other1.2266.3443380
X-RAY DIFFRACTIONr_mcangle_it2.2029.5154221
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 108 -
Rwork0.365 1988 -
all-2096 -
obs--99.76 %

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