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- PDB-5mkg: PA3825-EAL Ca-CdG Structure -

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Basic information

Entry
Database: PDB / ID: 5mkg
TitlePA3825-EAL Ca-CdG Structure
Components(Diguanylate phosphodiesterase) x 2
KeywordsHYDROLASE / EAL / Phosphodiesterase / biofilm formation / P Aeruginosa / PA3825
Function / homologyEAL domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Chem-C2E / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 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
DepositionDec 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
SupersessionMay 8, 2019ID: 4Y9O
Revision 1.2May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_database_PDB_obs_spr ...pdbx_data_processing_status / pdbx_database_PDB_obs_spr / pdbx_database_proc / struct_conn / struct_conn_type
Revision 1.3Jul 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_variant
Revision 1.4Jun 19, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,28311
Polymers56,6222
Non-polymers1,6619
Water1,36976
1
A: Diguanylate phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2215
Polymers28,4101
Non-polymers8114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diguanylate phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0626
Polymers28,2111
Non-polymers8515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.230, 59.400, 92.780
Angle α, β, γ (deg.)90.000, 115.030, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 6 - 259

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA2 - 255
2BB1 - 254

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Components

#1: Protein Diguanylate phosphodiesterase


Mass: 28410.430 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
#2: Protein Diguanylate phosphodiesterase


Mass: 28211.221 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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: 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.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 6-11% iso-propanol, 0.1 M Mes pH 6.5, 0.1 M sodium acetate pH 4.5 and 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.44→51.29 Å / Num. obs: 20405 / % possible obs: 98.3 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.026 / Rrim(I) all: 0.057 / Net I/σ(I): 17.3 / Num. measured all: 91744 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.44-2.54.80.8410.774199
10.91-51.294.30.0190.999195.9

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
MOLREPphasing
RefinementResolution: 2.44→51.29 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.206 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.683 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1060 5.2 %RANDOM
Rwork0.2377 ---
obs0.2401 19345 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.07 Å2 / Biso mean: 59.8 Å2 / Biso min: 28.64 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å2-0.99 Å2
2--1.81 Å2-0 Å2
3---1.77 Å2
Refinement stepCycle: final / Resolution: 2.44→51.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 99 76 4066
Biso mean--46.53 53.05 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194074
X-RAY DIFFRACTIONr_bond_other_d0.0020.023807
X-RAY DIFFRACTIONr_angle_refined_deg1.3732.0155545
X-RAY DIFFRACTIONr_angle_other_deg0.93338804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90623.315184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92215675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9281536
X-RAY DIFFRACTIONr_chiral_restr0.070.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02833
Refine LS restraints NCS

Ens-ID: 1 / Number: 13986 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.44→2.503 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 71 -
Rwork0.326 1420 -
all-1491 -
obs--98.94 %

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