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

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Basic information

Entry
Database: PDB / ID: 4etx
TitleCrystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1
ComponentsPelD
KeywordsSIGNALING PROTEIN / c-di-GMP
Function / homology
Function and homology information


cyclic-di-GMP binding / single-species biofilm formation
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 / SAD / 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 24, 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 / 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

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Assembly

Deposited unit
A: PelD


Theoretical massNumber of molelcules
Total (without water)33,7121
Polymers33,7121
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.290, 42.440, 60.470
Angle α, β, γ (deg.)90.000, 112.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PelD


Mass: 33712.344 Da / Num. of mol.: 1 / Fragment: UNP residues 155-454
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 8
Details: 100 mM Tris, pH 8, 200 mM MgCl2, 10% (v/v) PEG 8000, 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
ReflectionHighest resolution: 2 Å / Num. obs: 19307 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.15 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.10.4684.0417038259099.7
2.1-2.20.3116.73161442136100
2.2-2.30.2269.213655180599.8
2.3-2.50.14713.4821234280699.9
2.5-2.80.09319.9721453283399.9
2.8-3.30.05133.2620679273399.7
3.3-3.80.03349.3811277150799.7
3.8-4.60.02859.589302125099.7
4.6-5.50.02662.33487966699.6
5.5-80.02660.58473965899.8
8-500.02560.64195732398.2
50

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.015 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 965 5 %RANDOM
Rwork0.232 ---
obs0.2346 19298 100 %-
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: 84.25 Å2 / Biso mean: 42.27 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å2-0.67 Å2
2---1.47 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 0 86 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222401
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9973245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72223.071127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0131533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211847
X-RAY DIFFRACTIONr_mcbond_it0.7111.51487
X-RAY DIFFRACTIONr_mcangle_it1.29222363
X-RAY DIFFRACTIONr_scbond_it1.8483914
X-RAY DIFFRACTIONr_scangle_it3.064.5882
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 69 -
Rwork0.278 1309 -
all-1378 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -4.2278 Å / Origin y: 1.5679 Å / Origin z: 15.0848 Å
111213212223313233
T0.1383 Å2-0.006 Å20.0607 Å2-0.1471 Å20.0166 Å2--0.0997 Å2
L3.049 °20.3477 °22.3666 °2-0.9291 °20.6564 °2--2.4631 °2
S0.0412 Å °-0.1508 Å °-0.0585 Å °0.0602 Å °-0.0805 Å °0.1604 Å °0.0115 Å °-0.3187 Å °0.0393 Å °

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