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- PDB-4euv: Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1... -

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Basic information

Entry
Database: PDB / ID: 4euv
TitleCrystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1, in complex with c-di-GMP, form 1
ComponentsPelD
KeywordsSIGNALING PROTEIN / c-di-GMP
Function / homology
Function and homology information


cyclic-di-GMP binding / polysaccharide biosynthetic process / single-species biofilm formation / membrane
Similarity search - Function
Alpha-Beta Plaits - #2880 / PelD, GGDEF domain / PelD, GGDEF domain superfamily / PelD GGDEF domain / GAF domain / GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...Alpha-Beta Plaits - #2880 / PelD, GGDEF domain / PelD, GGDEF domain superfamily / PelD GGDEF domain / GAF domain / GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, Z. / Chen, J. / Nair, S.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structures of the PelD Cyclic Diguanylate Effector Involved in Pellicle Formation in Pseudomonas aeruginosa PAO1.
Authors: Li, Z. / Chen, J.H. / Hao, Y. / Nair, S.K.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0172
Polymers33,3271
Non-polymers6901
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.531, 41.516, 64.402
Angle α, β, γ (deg.)90.000, 110.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PelD


Mass: 33326.965 Da / Num. of mol.: 1 / Fragment: UNP residues 158-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3061, pelD / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3) / References: UniProt: Q9HZE7
#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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate, pH 6.5, 10 mM MgSO4, 1.3 M Li2SO4, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19997 / % possible obs: 99.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Χ2: 0.953 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.035.30.4029510.601195.1
2.03-2.075.40.3359660.622195
2.07-2.115.70.3359300.62197.1
2.11-2.155.80.310100.629199.4
2.15-2.260.27810100.645198.2
2.2-2.256.30.2659630.6631100
2.25-2.316.30.23610100.664198.8
2.31-2.376.50.2179850.6991100
2.37-2.446.60.210130.704199.7
2.44-2.526.90.1819830.706199.6
2.52-2.6170.18710120.704199.6
2.61-2.717.30.17510070.7511100
2.71-2.847.50.1589980.758199.6
2.84-2.997.50.13310060.787199.9
2.99-3.177.60.10810090.9131100
3.17-3.427.60.08510141.14199.9
3.42-3.767.50.07510191.701199.9
3.76-4.317.50.06610161.9981100
4.31-5.437.40.05210291.5091100
5.43-507.10.04510661.461199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.272 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 1022 5.1 %RANDOM
Rwork0.2205 ---
obs0.2236 19948 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 44.87 Å2 / Biso mean: 45.95 Å2 / Biso min: 2.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å2-2.22 Å2
2--0.15 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 46 128 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222337
X-RAY DIFFRACTIONr_angle_refined_deg1.5172.0273171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74122.966118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30715402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2691531
X-RAY DIFFRACTIONr_chiral_restr0.0920.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211771
X-RAY DIFFRACTIONr_mcbond_it0.6931.51418
X-RAY DIFFRACTIONr_mcangle_it1.2822254
X-RAY DIFFRACTIONr_scbond_it2.0133919
X-RAY DIFFRACTIONr_scangle_it3.1324.5917
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 72 -
Rwork0.258 1320 -
all-1392 -
obs--94.37 %
Refinement TLS params.Method: refined / Origin x: -3.1073 Å / Origin y: 0.7177 Å / Origin z: 17.6684 Å
111213212223313233
T0.1543 Å20.0296 Å20.0087 Å2-0.2362 Å2-0.0062 Å2--0.1532 Å2
L3.769 °21.0097 °21.3818 °2-1.9275 °20.7616 °2--2.6492 °2
S-0.101 Å °0.3598 Å °0.1043 Å °-0.273 Å °-0.0116 Å °0.3456 Å °-0.1232 Å °-0.5223 Å °0.1126 Å °

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