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- PDB-4y9n: PA3825-EAL Metal-Free-Apo Structure - Magnesium Co-crystallisation -

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Basic information

Entry
Database: PDB / ID: 4y9n
TitlePA3825-EAL Metal-Free-Apo Structure - Magnesium Co-crystallisation
ComponentsPA3825-EAL
KeywordsUNKNOWN FUNCTION / 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 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
PHOSPHATE ION / cyclic-guanylate-specific phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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: Structure of PA3825 from P. aeruginosa bound to cyclic di-GMP and pGpG: new insights for a potential three-metal catalytic mechanism of EAL domains
Authors: Bellini, D. / Horrell, S. / Wagner, A. / Strange, R. / Hutchin, 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: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / 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.occupancy / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PA3825-EAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2212
Polymers29,1261
Non-polymers951
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-3 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.440, 64.440, 134.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

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Components

#1: Protein PA3825-EAL


Mass: 29126.229 Da / Num. of mol.: 1
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
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: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→58.1 Å / Num. all: 22440 / Num. obs: 21243 / % possible obs: 99.92 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.1
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 3.6 / % possible all: 99.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→58.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.151 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22535 1132 5.1 %RANDOM
Rwork0.19298 ---
obs0.19465 21243 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.989 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.92→58.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 5 141 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192189
X-RAY DIFFRACTIONr_bond_other_d0.0020.022084
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9812990
X-RAY DIFFRACTIONr_angle_other_deg0.89134812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0435286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42923.069101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99715372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3351521
X-RAY DIFFRACTIONr_chiral_restr0.070.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212549
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
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_it1.6792.3421102
X-RAY DIFFRACTIONr_mcbond_other1.6762.3381101
X-RAY DIFFRACTIONr_mcangle_it2.2993.4871402
X-RAY DIFFRACTIONr_mcangle_other2.2993.4931403
X-RAY DIFFRACTIONr_scbond_it2.8742.7941087
X-RAY DIFFRACTIONr_scbond_other2.8642.791084
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5254.0351583
X-RAY DIFFRACTIONr_long_range_B_refined6.56619.9532488
X-RAY DIFFRACTIONr_long_range_B_other6.54619.5952437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 74 -
Rwork0.234 1548 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -8.318 Å / Origin y: 26.11 Å / Origin z: 24.098 Å
111213212223313233
T0.0478 Å2-0.0161 Å20.0176 Å2-0.0648 Å2-0.0017 Å2--0.0077 Å2
L0.9678 °2-0.323 °2-0.0863 °2-0.8141 °20.2125 °2--0.8052 °2
S0.0014 Å °0.0522 Å °0.0121 Å °-0.0091 Å °0.0097 Å °0.0183 Å °-0.0423 Å °-0.0138 Å °-0.0111 Å °

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