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- PDB-7lz3: Computational design of constitutively active cGAS -

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Basic information

Entry
Database: PDB / ID: 7lz3
TitleComputational design of constitutively active cGAS
ComponentsCyclic GMP-AMP synthase
KeywordsDE NOVO PROTEIN / DE NOVO DESIGNED / constitutive mutant / cGAS
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsDowling, Q. / Volkman, H.E. / Gray, E.E. / Ovchinnikov, S. / Cambier, S. / Bera, A.K. / Bick, M. / Kang, A. / Stetson, D.B. / King, N.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Computational design of constitutively active cGAS.
Authors: Dowling, Q.M. / Volkman, H.E. / Gray, E.E. / Ovchinnikov, S. / Cambier, S. / Bera, A.K. / Sankaran, B. / Johnson, M.R. / Bick, M.J. / Kang, A. / Stetson, D.B. / King, N.P.
History
DepositionMar 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,2357
Polymers84,8282
Non-polymers4075
Water3,729207
1
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6644
Polymers42,4141
Non-polymers2503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5723
Polymers42,4141
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.238, 106.363, 75.667
Angle α, β, γ (deg.)90.000, 91.132, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cyclic GMP-AMP synthase


Mass: 42414.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.45 M potassium thiocyanate, 0.1 M Bis-Tris propane pH 7.0, and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.18→47.23 Å / Num. obs: 38992 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 40.59 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.2
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2875 / CC1/2: 0.633 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3500refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→47.23 Å / SU ML: 0.3046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1671
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646 1910 4.9 %
Rwork0.2108 37047 -
obs0.2135 38957 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.62 Å2
Refinement stepCycle: LAST / Resolution: 2.18→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5773 0 20 207 6000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185926
X-RAY DIFFRACTIONf_angle_d0.45597948
X-RAY DIFFRACTIONf_chiral_restr0.038853
X-RAY DIFFRACTIONf_plane_restr0.0031002
X-RAY DIFFRACTIONf_dihedral_angle_d15.03393656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.32371210.26982602X-RAY DIFFRACTION98.59
2.23-2.30.34821160.27982656X-RAY DIFFRACTION99.89
2.3-2.360.34161380.26772688X-RAY DIFFRACTION99.96
2.36-2.440.28761240.25522601X-RAY DIFFRACTION99.89
2.44-2.530.33611490.24712657X-RAY DIFFRACTION99.89
2.53-2.630.31951190.24572647X-RAY DIFFRACTION99.96
2.63-2.750.25341480.23822613X-RAY DIFFRACTION99.96
2.75-2.890.2961460.23332645X-RAY DIFFRACTION100
2.89-3.070.29151380.23112639X-RAY DIFFRACTION100
3.07-3.310.29911350.22452655X-RAY DIFFRACTION99.89
3.31-3.640.24421380.20172658X-RAY DIFFRACTION100
3.64-4.170.22591320.18682634X-RAY DIFFRACTION100
4.17-5.250.23611470.17632674X-RAY DIFFRACTION100

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