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- PDB-3bre: Crystal Structure of P.aeruginosa PA3702 -

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Basic information

Entry
Database: PDB / ID: 3bre
TitleCrystal Structure of P.aeruginosa PA3702
ComponentsProbable two-component response regulator
KeywordsSIGNALING PROTEIN / protein-nucleotide complex
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / phosphorelay signal transduction system / nucleotide binding / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / diguanylate cyclase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsDe, N. / Pirruccello, M. / Krasteva, P.V. / Bae, N. / Raghavan, R.V. / Sondermann, H.
CitationJournal: Plos Biol. / Year: 2008
Title: Phosphorylation-independent regulation of the diguanylate cyclase WspR.
Authors: De, N. / Pirruccello, M. / Krasteva, P.V. / Bae, N. / Raghavan, R.V. / Sondermann, H.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Probable two-component response regulator
B: Probable two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2378
Polymers78,4272
Non-polymers2,8106
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
MethodPISA
2
A: Probable two-component response regulator
B: Probable two-component response regulator
hetero molecules

A: Probable two-component response regulator
B: Probable two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,47416
Polymers156,8534
Non-polymers5,62112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)144.510, 72.748, 106.095
Angle α, β, γ (deg.)90.000, 110.790, 90.000
Int Tables number5
Space group name H-MC121
Detailstwo C2-crystal symmetry-related dimers (chains A,B) form a biological unit (tetramer)

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Components

#1: Protein Probable two-component response regulator


Mass: 39213.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: wspR / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9HXT9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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 / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2

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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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-Cl pH8.0, 2.9M NaCl, 15% xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 18, 2006 / Details: mirrors
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 12.3 / Number: 171005 / Rmerge(I) obs: 0.066 / Χ2: 1.01 / D res high: 2.39 Å / D res low: 50 Å / Num. obs: 40110 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.155099.510.0391.0364.4
4.095.1510010.0521.0184.4
3.574.0995.310.0711.0483.7
3.243.5710010.0881.0544.5
3.013.2410010.1081.0544.6
2.833.0110010.1531.0684.6
2.692.8310010.2271.0434.6
2.572.6910010.3150.9754.6
2.482.5799.910.450.8834.1
2.392.4894.510.4590.8713
ReflectionResolution: 2.39→50 Å / Num. obs: 40110 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.049 / Χ2: 1.012 / Net I/σ(I): 12.3
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2 / Num. unique all: 3803 / Rsym value: 0.459 / Χ2: 0.871 / % possible all: 94.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.41 Å
Translation2.5 Å48.41 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W25

1w25


Resolution: 2.4→33.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 84696.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2707 7.3 %RANDOM
Rwork0.242 ---
obs-37059 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.73 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 67.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.07 Å20 Å2-15.11 Å2
2--7.92 Å20 Å2
3----3.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.4→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 186 0 5182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 372 7.2 %
Rwork0.363 4801 -
all-5173 -
obs--77.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cdg.parcdg.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.param

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