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- PDB-9ild: Complex structure of Cap3 and CD-NTase -

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Basic information

Entry
Database: PDB / ID: 9ild
TitleComplex structure of Cap3 and CD-NTase
Components
  • Cyclic GMP-AMP synthase
  • Peptidase
KeywordsANTIFUNGAL PROTEIN / CD-NTase / cGAS / CD-NTase conjugation / Cap2 / Cap3 / CBASS
Function / homology
Function and homology information


3',3'-cyclic GMP-AMP synthase activity / nucleotide metabolic process / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function
CD-NTase-associated protein 3 / JAB domain, prokaryotic / Prokaryotic homologs of the JAB domain / : / : / Cyclic GMP-AMP synthase, C-terminal domain / : / Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain
Similarity search - Domain/homology
Peptidase / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.179 Å
AuthorsLi, F.Q. / Ma, W.F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural and functional characterization of the bacterial Cap3 enzyme in deconjugation and regulation of the cyclic dinucleotide transferase CD-NTase
Authors: Li, F.Q. / Ma, W.F.
History
DepositionJun 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0863
Polymers21,0202
Non-polymers651
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-51 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.051, 54.843, 59.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidase / Cap3


Mass: 18123.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GOP25_26465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3J1GR98
#2: Protein/peptide Cyclic GMP-AMP synthase / CD-NTase


Mass: 2896.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ETECE562_01214 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7I8YYL1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NH4Ac, 0.1 M NaAc (pH 4.6) and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.179→39.206 Å / Num. obs: 9260 / % possible obs: 98.5 % / Redundancy: 13.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.1
Reflection shellResolution: 2.179→2.3 Å / Rmerge(I) obs: 0.839 / Num. unique obs: 1210 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.179→39.206 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 915 9.92 %
Rwork0.2282 --
obs0.2333 9220 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.179→39.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 1 48 1482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031474
X-RAY DIFFRACTIONf_angle_d0.4771988
X-RAY DIFFRACTIONf_dihedral_angle_d2.739892
X-RAY DIFFRACTIONf_chiral_restr0.047216
X-RAY DIFFRACTIONf_plane_restr0.003256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.179-2.29370.33851080.28371069X-RAY DIFFRACTION90
2.2937-2.43740.32651380.26531161X-RAY DIFFRACTION100
2.4374-2.62550.32031310.28091192X-RAY DIFFRACTION100
2.6255-2.88970.31411300.26171189X-RAY DIFFRACTION100
2.8897-3.30760.27571360.24211191X-RAY DIFFRACTION100
3.3076-4.16650.28061330.20361219X-RAY DIFFRACTION100
4.1665-39.2060.24491390.20031284X-RAY DIFFRACTION100

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