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- PDB-5mfu: PA3825-EAL Mn-pGpG Structure -

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Basic information

Entry
Database: PDB / ID: 5mfu
TitlePA3825-EAL Mn-pGpG Structure
Components
  • RNA (pGpG)
  • cyclic-guanylate-specific phosphodiesterase
KeywordsHYDROLASE / EAL / Phosphodiesterase / biofilm formation / P Aeruginosa / PA3825
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / regulation of single-species biofilm formation / 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 profile. / EAL domain / TIM Barrel ...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 profile. / EAL domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / RNA / cyclic-guanylate-specific phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Source and taxonomy / Category: database_PDB_remark / entity_src_gen
Item: _database_PDB_remark.text / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._database_PDB_remark.text / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 2.0Dec 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity.type / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cyclic-guanylate-specific phosphodiesterase
B: RNA (pGpG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9494
Polymers28,8712
Non-polymers782
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.780, 64.780, 135.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein cyclic-guanylate-specific phosphodiesterase


Mass: 28225.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3825 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21
References: UniProt: Q9HXH7, cyclic-guanylate-specific phosphodiesterase
#2: RNA chain RNA (pGpG)


Mass: 645.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 51.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 6-11% isopropanol, 0.1 M MES pH 6.5, 0.1 M sodium acetate pH 4.5 and 0.2 M MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.8785 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: 1.8785 Å / Relative weight: 1
ReflectionResolution: 2.15→27.16 Å / Num. obs: 16288 / % possible obs: 98.8 % / Redundancy: 3.8 % / Net I/σ(I): 6.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
PDB_EXTRACT3.2data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y9M

4y9m


Resolution: 2.15→26.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.728 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 808 5 %RANDOM
Rwork0.2021 ---
obs0.2051 15439 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.96 Å2 / Biso mean: 36.452 Å2 / Biso min: 13.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å2-0 Å2-0 Å2
2--1.29 Å2-0 Å2
3----2.58 Å2
Refinement stepCycle: final / Resolution: 2.15→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 49 118 2153
Biso mean--30.43 37.66 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192142
X-RAY DIFFRACTIONr_bond_other_d0.0060.022038
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9642924
X-RAY DIFFRACTIONr_angle_other_deg1.03434692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73522.88797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72815357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0121521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212411
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02488
X-RAY DIFFRACTIONr_mcbond_it3.3583.361045
X-RAY DIFFRACTIONr_mcbond_other3.363.3571044
X-RAY DIFFRACTIONr_mcangle_it5.3875.021315
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 55 -
Rwork0.269 1114 -
all-1169 -
obs--99.24 %

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