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- PDB-8z84: The dimerization structure of CHASE4 domain of PA2072(beta form). -

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Basic information

Entry
Database: PDB / ID: 8z84
TitleThe dimerization structure of CHASE4 domain of PA2072(beta 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: 2.17 Å
AuthorsZhang, Y. / Lin, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The dimerization structure of CHASE4 domain of PA2072(beta form).
Authors: Zhang, Y. / Lin, Z.
History
DepositionApr 21, 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
Water2,486138
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
Buried area3060 Å2
ΔGint-3 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.382, 74.280, 101.797
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.: 138 / 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: 2.74 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350,10 mM MgCl2, 2 mM adenosine triphosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. obs: 12066 / % possible obs: 91.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 23.24 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.3
Reflection shellResolution: 2.17→2.21 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 587 / CC1/2: 0.822

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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: 2.17→20 Å / SU ML: 0.2705 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 599 4.97 %
Rwork0.2232 11449 -
obs0.225 12048 91.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.88 Å2
Refinement stepCycle: LAST / Resolution: 2.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 0 140 1750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951641
X-RAY DIFFRACTIONf_angle_d1.04462227
X-RAY DIFFRACTIONf_chiral_restr0.0569249
X-RAY DIFFRACTIONf_plane_restr0.007291
X-RAY DIFFRACTIONf_dihedral_angle_d13.293229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.390.34121350.28922790X-RAY DIFFRACTION89.83
2.39-2.740.3331570.272880X-RAY DIFFRACTION93.22
2.74-3.440.26711510.22062890X-RAY DIFFRACTION93.05
3.45-200.19871560.18582889X-RAY DIFFRACTION89.04
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.747894487170.5563043207080.07785543627120.7573168091560.3239678145271.295285509160.17516425454-0.277260598279-0.4263807731520.2002883699730.166238783028-0.388741858760.1647368470060.568630680203-0.2057724886550.1757988561510.0360797778084-0.07850701174860.330115416358-0.1516414402210.4287209846056.34295587941-5.6940578904522.6829551001
21.03709101016-0.546138003211-0.156587563013.117554883581.865564222872.693528956560.2459290441590.23107708852-0.0196346253113-1.24829588645-1.090585018760.739719459126-0.724026210717-1.593865777440.33238110475-0.1138622818150.00939467869662-0.05042054355660.580662997795-0.2465996695060.335649512205-21.1156729833-5.6299819727812.9868891082
31.551860972980.05455502984190.1188781678391.86542000651.53967721272.692833832620.1802653529740.0151190300927-0.08290910468670.479335193825-0.4384629393220.2647708114150.765473762332-0.5904325880510.03472475672150.313129408667-0.1973274584040.1031063882130.229441175622-0.0898412597610.247720455032-14.5846240967-13.331839234819.0787575509
40.9833784522930.1417206399510.9588142415682.172308296830.7617784077442.510929313280.08509554635750.09987402580130.138645946031-0.1851244970390.235391597925-0.495703955522-0.4055585206570.687956460302-0.274355281880.214199829263-0.0735620295310.08914709826560.355572058903-0.08014524513170.3550560178458.75972661256-1.8763344707513.1004487668
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 39 through 75 )39 - 751 - 37
22chain 'A' and (resid 76 through 141 )76 - 14138 - 103
33chain 'A' and (resid 142 through 201 )142 - 201104 - 163
44chain 'A' and (resid 202 through 251 )202 - 251164 - 208

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