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- PDB-7e6g: Crystal structure of diguanylate cyclase SiaD in complex with its... -

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Basic information

Entry
Database: PDB / ID: 7e6g
TitleCrystal structure of diguanylate cyclase SiaD in complex with its activator SiaC from Pseudomonas aeruginosa
Components
  • DUF1987 domain-containing protein
  • Putative GGDEF domain protein
KeywordsDE NOVO PROTEIN / diguanylate cyclase / activation / Pseudomonas aeruginosa / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


diguanylate cyclase / metal ion binding
Similarity search - Function
SiaC family regulatory phosphoprotein / SiaC family regulatory phosphoprotein / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain ...SiaC family regulatory phosphoprotein / SiaC family regulatory phosphoprotein / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / diguanylate cyclase / Biofilm formation regulator SiaD modulator protein SiaC
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZhou, J.S. / Zhang, L. / Zhang, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21722802 China
National Natural Science Foundation of China (NSFC)91853118 China
CitationJournal: Elife / Year: 2021
Title: Structural basis for diguanylate cyclase activation by its binding partner in Pseudomonas aeruginosa .
Authors: Chen, G. / Zhou, J. / Zuo, Y. / Huo, W. / Peng, J. / Li, M. / Zhang, Y. / Wang, T. / Zhang, L. / Zhang, L. / Liang, H.
History
DepositionFeb 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative GGDEF domain protein
B: Putative GGDEF domain protein
C: DUF1987 domain-containing protein
D: DUF1987 domain-containing protein
E: DUF1987 domain-containing protein
F: DUF1987 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3428
Polymers121,7976
Non-polymers5462
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-74 kcal/mol
Surface area49070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.525, 236.728, 148.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative GGDEF domain protein / Response regulator PleD


Mass: 31587.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pleD_3, pleD_1, pleD_4, NCTC12951_03415, NCTC13437_04900, NCTC13621_04785, PAMH19_0165, RW109_RW109_00771
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069QEY1
#2: Protein
DUF1987 domain-containing protein / SiaC


Mass: 14655.237 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZHB4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Spermidine trihydrochloride and 15% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 40897 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 0.982 / Net I/σ(I): 13.1
Reflection shellResolution: 2.65→2.74 Å / Num. unique obs: 4204 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I5A

3i5a


Resolution: 2.65→46.295 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 2087 5.1 %
Rwork0.2177 38810 -
obs0.2201 40897 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.86 Å2 / Biso mean: 55.2951 Å2 / Biso min: 11.88 Å2
Refinement stepCycle: final / Resolution: 2.65→46.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8233 0 33 197 8463
Biso mean--52.17 42.15 -
Num. residues----1016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.65-2.71130.3441970.3125169064
2.7113-2.7790.35661210.2857235987
2.779-2.85420.36571260.2859243491
2.8542-2.93810.31171530.284261299
2.9381-3.0330.32311270.2741266799
3.033-3.14130.36881380.259267599
3.1413-3.26710.29721570.24522630100
3.2671-3.41570.30691470.22342683100
3.4157-3.59580.25941230.23172728100
3.5958-3.82090.24811490.2093264699
3.8209-4.11580.23451470.19422707100
4.1158-4.52970.23141470.18122714100
4.5297-5.18440.23141360.17742740100
5.1844-6.52880.25671540.2222269098
6.5288-46.2950.20511650.1817283599

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