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- PDB-5xgd: Crystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseu... -

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Basic information

Entry
Database: PDB / ID: 5xgd
TitleCrystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseudomonas aeruginosa in complex with GTP
ComponentsUncharacterized protein PA0861
KeywordsTRANSCRIPTION / PAS domain / GGDEF-EAL domain / Pseudomonas aeruginosa / Biofilm / RbdA / PA0861 / GTP
Function / homology
Function and homology information


regulation of DNA-templated transcription / GTP binding / membrane / metal ion binding
Similarity search - Function
Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase ...Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / EAL domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLiu, C. / Liew, C.W. / Sreekanth, R. / Lescar, J.
CitationJournal: J. Bacteriol. / Year: 2018
Title: Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa.
Authors: Liu, C. / Liew, C.W. / Wong, Y.H. / Tan, S.T. / Poh, W.H. / Manimekalai, M.S.S. / Rajan, S. / Xin, L. / Liang, Z.X. / Gruber, G. / Rice, S.A. / Lescar, J.
History
DepositionApr 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.4Mar 27, 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: Uncharacterized protein PA0861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0333
Polymers63,4851
Non-polymers5472
Water5,224290
1
A: Uncharacterized protein PA0861
hetero molecules

A: Uncharacterized protein PA0861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0666
Polymers126,9712
Non-polymers1,0954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area9660 Å2
ΔGint-78 kcal/mol
Surface area47600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.729, 134.729, 209.953
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1201-

HOH

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Components

#1: Protein Uncharacterized protein PA0861


Mass: 63485.305 Da / Num. of mol.: 1 / Fragment: UNP residues 233-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0861 / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9I580
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES/imidazole at pH 6.5, 0.1M carboxylic acid, 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→47.9 Å / Num. obs: 18306 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 55.41 Å2 / Rmerge(I) obs: 0.276 / Net I/σ(I): 9.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.8→27.55 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.847 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.252 935 5.11 %RANDOM
Rwork0.177 ---
obs0.181 18292 100 %-
Displacement parametersBiso mean: 45.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.909 Å20 Å20 Å2
2--1.909 Å20 Å2
3----3.818 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 33 290 4617
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094405HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.145971HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1567SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it4405HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion20.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion572SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5228SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2627 143 4.9 %
Rwork0.2009 2774 -
all0.2041 2917 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 39.9147 Å / Origin y: 0.9178 Å / Origin z: 90.8629 Å
111213212223313233
T-0.0958 Å20.0107 Å20.0517 Å2--0.048 Å2-0.0562 Å2---0.1564 Å2
L0.9376 °20.0699 °20.2505 °2-0.3756 °20.0888 °2--1.043 °2
S0.0142 Å °0.0186 Å °0.0746 Å °-0.0589 Å °0.0397 Å °-0.0817 Å °-0.0905 Å °0.1391 Å °-0.0539 Å °
Refinement TLS groupSelection details: { A|* }

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