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- PDB-8z6n: The dimerization structure of CHASE4 domain of PA2072 (alpha form) -

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Basic information

Entry
Database: PDB / ID: 8z6n
TitleThe dimerization structure of CHASE4 domain of PA2072 (alpha form)
ComponentsBifunctional diguanylate cyclase/phosphodiesterase
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


CHASE4 / CHASE4 domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase ...CHASE4 / CHASE4 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 domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Bifunctional diguanylate cyclase/phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsZhang, Y. / Lin, Z. / Xiao, Y.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The dimerization structure of CHASE4 domain of PA2072.
Authors: Zhang, Y. / Lin, Z.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional diguanylate cyclase/phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)23,7161
Polymers23,7161
Non-polymers00
Water1,910106
1
A: Bifunctional diguanylate cyclase/phosphodiesterase

A: Bifunctional diguanylate cyclase/phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)47,4332
Polymers47,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Unit cell
Length a, b, c (Å)64.552, 75.945, 103.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Bifunctional diguanylate cyclase/phosphodiesterase


Mass: 23716.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA2072 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I243
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.385→50 Å / Num. obs: 10273 / % possible obs: 98.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.52 Å2 / Rrim(I) all: 0.067 / Net I/σ(I): 22.2
Reflection shellResolution: 2.39→2.44 Å / Num. unique obs: 459 / CC1/2: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→24.59 Å / SU ML: 0.253 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 490 4.77 %
Rwork0.1827 9775 -
obs0.1846 10265 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.39 Å2
Refinement stepCycle: LAST / Resolution: 2.39→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 0 106 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00191593
X-RAY DIFFRACTIONf_angle_d0.47652163
X-RAY DIFFRACTIONf_chiral_restr0.0397243
X-RAY DIFFRACTIONf_plane_restr0.0026282
X-RAY DIFFRACTIONf_dihedral_angle_d19.4542566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.730.22971590.18483128X-RAY DIFFRACTION96.59
2.73-3.440.21191600.17323280X-RAY DIFFRACTION99.05
3.44-24.590.22081710.18753367X-RAY DIFFRACTION98.74

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