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- PDB-6e0m: Structure of Elizabethkingia meningoseptica CdnE cyclic dinucleot... -

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Basic information

Entry
Database: PDB / ID: 6e0m
TitleStructure of Elizabethkingia meningoseptica CdnE cyclic dinucleotide synthase
ComponentscGAS/DncV-like nucleotidyltransferase in E. coli homolog
KeywordsTRANSFERASE / cGAS / DncV / cyclic dinucleotide / nucleotide second messenger / nucleotidyltransferase
Function / homology
Function and homology information


3',3'-cyclic GMP-AMP synthase activity / diguanylate cyclase / diadenylate cyclase / diguanylate cyclase activity / diadenylate cyclase activity / nucleotide metabolic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
DIPHOSPHATE / Cyclic dipurine nucleotide synthase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica ATCC 13253 = NBRC 12535 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsEaglesham, J.B. / Whiteley, A.T. / de Oliveira Mann, C.C. / Morehouse, B.R. / Nieminen, E.A. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI018045 United States
CitationJournal: Nature / Year: 2019
Title: Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.
Authors: Whiteley, A.T. / Eaglesham, J.B. / de Oliveira Mann, C.C. / Morehouse, B.R. / Lowey, B. / Nieminen, E.A. / Danilchanka, O. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGAS/DncV-like nucleotidyltransferase in E. coli homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3732
Polymers34,1991
Non-polymers1741
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.195, 58.231, 99.446
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 cGAS/DncV-like nucleotidyltransferase in E. coli homolog


Mass: 34199.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica ATCC 13253 = NBRC 12535 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P0DSP2*PLUS
#2: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16% PEG-5000 MME, 21 mM sodium citrate pH 7.0, 100 mM HEPES-KOH pH 7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.52→49.58 Å / Num. obs: 52028 / % possible obs: 99.8 % / Redundancy: 12.9 % / Rpim(I) all: 0.033 / Net I/av σ(I): 13.6 / Net I/σ(I): 13.6
Reflection shellResolution: 1.52→1.54 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2474 / Rpim(I) all: 0.623 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→40.804 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 2004 3.86 %5
Rwork0.1396 ---
obs0.1409 51875 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.52→40.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 9 326 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072308
X-RAY DIFFRACTIONf_angle_d0.8183127
X-RAY DIFFRACTIONf_dihedral_angle_d11.0321391
X-RAY DIFFRACTIONf_chiral_restr0.052340
X-RAY DIFFRACTIONf_plane_restr0.005409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5182-1.55620.28721350.22993382X-RAY DIFFRACTION96
1.5562-1.59830.2331350.17943518X-RAY DIFFRACTION100
1.5983-1.64530.20651470.15263531X-RAY DIFFRACTION100
1.6453-1.69840.19081400.14183519X-RAY DIFFRACTION100
1.6984-1.75910.21841420.14883544X-RAY DIFFRACTION100
1.7591-1.82950.21511400.13533536X-RAY DIFFRACTION100
1.8295-1.91280.18531410.1293552X-RAY DIFFRACTION100
1.9128-2.01370.14891470.11653548X-RAY DIFFRACTION100
2.0137-2.13980.15861420.11463555X-RAY DIFFRACTION100
2.1398-2.3050.16731470.1133567X-RAY DIFFRACTION100
2.305-2.53690.16531410.11963570X-RAY DIFFRACTION100
2.5369-2.9040.17451490.13393612X-RAY DIFFRACTION100
2.904-3.65830.16341490.14113632X-RAY DIFFRACTION100
3.6583-40.8190.16971490.15933805X-RAY DIFFRACTION100

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