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- PDB-4y9p: PA3825-EAL Ca-CdG Structure -

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Basic information

Entry
Database: PDB / ID: 4y9p
TitlePA3825-EAL Ca-CdG Structure
ComponentsPA3825-EAL
KeywordsSIGNALING PROTEIN / EAL / cyclic di-GMP
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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsBellini, D. / Horrell, S. / Wagner, A. / Strange, R. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: MucR and PA3825 EAL-phosphodiesterase domains from Pseudomonas aeruginosa suggest roles for three metals in the active site
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
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / 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 / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 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_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

Downloads & links

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Assembly

Deposited unit
A: PA3825-EAL
B: PA3825-EAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,87410
Polymers58,2522
Non-polymers1,6218
Water1,00956
1
A: PA3825-EAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9375
Polymers29,1261
Non-polymers8114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PA3825-EAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9375
Polymers29,1261
Non-polymers8114
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.)90.00, 115.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A6 - 262
2010B6 - 262

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Components

#1: Protein PA3825-EAL


Mass: 29126.229 Da / Num. of mol.: 2 / Fragment: UNP residues 255-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3825 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXH7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.86 %
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 2M / 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→84.07 Å / Num. all: 20405 / Num. obs: 19345 / % possible obs: 98.05 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.3
Reflection shellResolution: 2.44→2.503 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 2 / % possible all: 98.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y8E

4y8e


Resolution: 2.44→84.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 21.255 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24651 1060 5.2 %RANDOM
Rwork0.18795 ---
obs0.19094 19345 98.05 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-0.34 Å2
2--0.4 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.44→84.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3931 0 98 56 4085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194142
X-RAY DIFFRACTIONr_bond_other_d0.0080.023950
X-RAY DIFFRACTIONr_angle_refined_deg1.9992.0135640
X-RAY DIFFRACTIONr_angle_other_deg1.50939088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8695505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22523.209187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62715687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1681538
X-RAY DIFFRACTIONr_chiral_restr0.1070.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214609
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02929
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7734.3722023
X-RAY DIFFRACTIONr_mcbond_other5.7544.3712022
X-RAY DIFFRACTIONr_mcangle_it7.8196.5362527
X-RAY DIFFRACTIONr_mcangle_other7.826.542528
X-RAY DIFFRACTIONr_scbond_it7.1364.9812119
X-RAY DIFFRACTIONr_scbond_other7.1254.9822118
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1527.243114
X-RAY DIFFRACTIONr_long_range_B_refined13.20936.4174723
X-RAY DIFFRACTIONr_long_range_B_other13.20836.424724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28262 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 71 -
Rwork0.278 1421 -
obs--98.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6479-0.3626-0.02873.06281.02642.0896-0.041-0.1016-0.2977-0.11830.01-0.45290.23490.23290.0310.1496-0.01840.0390.08290.07680.1937-0.042-0.945-21.387
23.31190.03760.31822.6506-0.85043.4189-0.069-0.2492-0.2260.07550.03110.34250.5691-0.44110.03790.1523-0.06940.05050.0761-0.00190.0704-35.011-0.703-19.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 262
2X-RAY DIFFRACTION2B6 - 262

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