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- PDB-8u0i: Crystal structure of PA0012 complexed with cyclic-di-GMP from Pse... -

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Basic information

Entry
Database: PDB / ID: 8u0i
TitleCrystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa
ComponentsPilZ domain-containing protein
KeywordsSIGNALING PROTEIN / Complex
Function / homologyPilZ domain / PilZ domain / cyclic-di-GMP binding / Chem-C2E / PilZ domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.541 Å
AuthorsHammons, N.A. / Schnicker, N.J. / Fuentes, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)1R01AI170557-01A1 United States
CitationJournal: To Be Published
Title: Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa
Authors: Hammons, N.A. / Schnicker, N.J. / Fuentes, E.J.
History
DepositionAug 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PilZ domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6276
Polymers9,9691
Non-polymers1,6575
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.317, 50.317, 90.596
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

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Components

#1: Protein PilZ domain-containing protein


Mass: 9969.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA0012 / Plasmid: pET21a
Details (production host): Modified with an N-terminal cleavable hexa-His tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): K-12 / References: UniProt: Q9I7B4
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 57.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5.3 mg/mL PA0012 and 2.5 mM cyclic-di-GMP. 0.2 M NH4SO4, 15% (w/v) PEG4000, 0.1 M Tri-NaCit pH=5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0004 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.54→43.99 Å / Num. obs: 17945 / % possible obs: 100 % / Redundancy: 39.2 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.013 / Rrim(I) all: 0.083 / Χ2: 0.27 / Net I/σ(I): 19
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 32.9 % / Rmerge(I) obs: 1.064 / Num. unique obs: 865 / CC1/2: 0.971 / Rpim(I) all: 0.187 / Rrim(I) all: 1.08 / Χ2: 0.01 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.541→43.988 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.155 / SU B: 1.612 / SU ML: 0.055 / Average fsc free: 0.9656 / Average fsc work: 0.9708 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 873 4.881 %RANDOM
Rwork0.1733 17012 --
all0.175 ---
obs-17885 99.989 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.631 Å20 Å2-0 Å2
2--0.631 Å2-0 Å2
3----1.262 Å2
Refinement stepCycle: LAST / Resolution: 1.541→43.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 110 91 864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.012803
X-RAY DIFFRACTIONr_bond_other_d0.0010.016721
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.8371115
X-RAY DIFFRACTIONr_angle_other_deg0.7441.7471672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.33556
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.51654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45710118
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.981029
X-RAY DIFFRACTIONr_chiral_restr0.1130.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02162
X-RAY DIFFRACTIONr_nbd_refined0.1910.2119
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.2734
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2387
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.211
X-RAY DIFFRACTIONr_nbd_other0.2110.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0870.216
X-RAY DIFFRACTIONr_mcbond_it2.6292.425346
X-RAY DIFFRACTIONr_mcbond_other2.6282.418345
X-RAY DIFFRACTIONr_mcangle_it3.9314.319433
X-RAY DIFFRACTIONr_mcangle_other3.9284.318433
X-RAY DIFFRACTIONr_scbond_it3.8892.806457
X-RAY DIFFRACTIONr_scbond_other3.892.808458
X-RAY DIFFRACTIONr_scangle_it5.7144.929679
X-RAY DIFFRACTIONr_scangle_other5.7094.93680
X-RAY DIFFRACTIONr_lrange_it6.97130.04932
X-RAY DIFFRACTIONr_lrange_other6.97730.045933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.541-1.5810.268510.30112500.313030.9080.91799.84650.294
1.581-1.6240.24690.27211930.2712620.9630.9381000.261
1.624-1.6710.327580.23311570.23712150.9320.9561000.215
1.671-1.7230.219440.21711440.21711880.9610.9651000.195
1.723-1.7790.248660.19710930.211590.9640.9711000.17
1.779-1.8410.206530.1910500.19111030.9760.9761000.162
1.841-1.9110.236490.17610430.17910920.9680.9791000.145
1.911-1.9890.198550.16510020.16710570.9760.9821000.135
1.989-2.0770.173460.1679480.1679940.9780.9831000.139
2.077-2.1780.159440.1499250.1499690.9850.9871000.126
2.178-2.2960.184490.1588880.1599370.980.9861000.133
2.296-2.4340.243400.1548130.1588530.9660.9841000.129
2.434-2.6020.193460.1717870.1728330.9780.9821000.143
2.602-2.810.233510.1737360.1777870.9680.9811000.144
2.81-3.0760.25380.1686690.1727070.960.9821000.144
3.076-3.4370.207280.1636300.1646580.9780.9841000.146
3.437-3.9650.168310.1435610.1445920.9840.9881000.135
3.965-4.8470.212250.1414820.1445070.9760.9891000.136
4.847-6.8130.23170.2083910.2094080.9820.9811000.198
6.813-43.9880.186130.2292500.2272630.9730.9721000.228

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