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

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Basic information

Entry
Database: PDB / ID: 5xgb
TitleCrystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseudomonas aeruginosa
ComponentsUncharacterized protein
KeywordsTRANSCRIPTION / PAS domain / GGDEF-EAL domain / Pseudomonas aeruginosa / Biofilm / RbdA / PA0861
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 profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain ...: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / 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
EAL domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.28 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 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Oct 17, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.4Apr 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 1.5Mar 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


Theoretical massNumber of molelcules
Total (without water)63,4851
Polymers63,4851
Non-polymers00
Water5,459303
1
A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)126,9712
Polymers126,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area7650 Å2
ΔGint-48 kcal/mol
Surface area48080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.720, 134.720, 210.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Uncharacterized protein


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) / Variant (production host): Rosetta DE3 / References: UniProt: Q9I580
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/imidazole at pH 6.5, 0.1 M carboxylic acid, 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→70.2 Å / Num. obs: 33717 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Net I/σ(I): 10.7
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4851 / CC1/2: 0.517 / Rpim(I) all: 0.454 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPBALBES, BUCANEERphasing
RefinementResolution: 2.28→70.15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.193
RfactorNum. reflection% reflectionSelection details
Rfree0.229 818 2.43 %RANDOM
Rwork0.193 ---
obs0.194 33717 100 %-
Displacement parametersBiso mean: 52.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.5459 Å20 Å20 Å2
2---1.5459 Å20 Å2
3---3.0917 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.28→70.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4318 0 0 303 4621
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014395HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.115950HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1563SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes645HARMONIC5
X-RAY DIFFRACTIONt_it4395HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion19.35
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_contact5146SEMIHARMONIC4
LS refinement shellResolution: 2.28→2.35 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.276 -2.25 %
Rwork0.2236 2819 -
all0.2246 2884 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 40.1164 Å / Origin y: 0.8088 Å / Origin z: 91.2216 Å
111213212223313233
T-0.0932 Å20.0065 Å20.0462 Å2--0.0514 Å2-0.0499 Å2---0.1014 Å2
L0.8098 °20.1288 °20.2023 °2-0.3488 °20.1187 °2--0.9511 °2
S0.0222 Å °0.0199 Å °0.0359 Å °-0.0381 Å °0.0308 Å °-0.0583 Å °-0.1018 Å °0.1171 Å °-0.053 Å °
Refinement TLS groupSelection details: { A|* }

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