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- PDB-6wt9: Structure of STING-associated CdnE c-di-GMP synthase from Capnocy... -

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Basic information

Entry
Database: PDB / ID: 6wt9
TitleStructure of STING-associated CdnE c-di-GMP synthase from Capnocytophaga granulosa
ComponentsNTP_transf_2 domain-containing protein
KeywordsTRANSFERASE / CBASS / CD-NTase / c-di-GMP / STING
Function / homologydiguanylate cyclase / diguanylate cyclase activity / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily / defense response to virus / GTP binding / c-di-GMP synthase
Function and homology information
Biological speciesCapnocytophaga granulosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMorehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2020
Title: STING cyclic dinucleotide sensing originated in bacteria.
Authors: Morehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NTP_transf_2 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)41,3781
Polymers41,3781
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.998, 48.879, 59.704
Angle α, β, γ (deg.)90.000, 92.506, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein NTP_transf_2 domain-containing protein / CgCdnE


Mass: 41378.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga granulosa (bacteria) / Gene: NCTC12948_02564 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A381HBN1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium thiocyanate, 20% PEG-3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→44.85 Å / Num. obs: 14608 / % possible obs: 99.6 % / Redundancy: 10.4 % / Biso Wilson estimate: 18.54 Å2 / CC1/2: 0.961 / Rpim(I) all: 0.096 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1408 / CC1/2: 0.769 / Rpim(I) all: 0.457

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.85 Å / SU ML: 0.2445 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6953
RfactorNum. reflection% reflection
Rfree0.2396 1462 10.08 %
Rwork0.1859 --
obs0.1915 14499 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 0 169 2644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172510
X-RAY DIFFRACTIONf_angle_d0.41053374
X-RAY DIFFRACTIONf_chiral_restr0.0376378
X-RAY DIFFRACTIONf_plane_restr0.0018431
X-RAY DIFFRACTIONf_dihedral_angle_d15.9257975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.28681490.20911224X-RAY DIFFRACTION95.08
2.38-2.480.30921340.19851303X-RAY DIFFRACTION97.62
2.48-2.590.25891470.19981300X-RAY DIFFRACTION99.04
2.59-2.730.2671440.19841298X-RAY DIFFRACTION99.31
2.73-2.90.27611470.21091297X-RAY DIFFRACTION99.45
2.9-3.120.22771480.20011306X-RAY DIFFRACTION99.38
3.12-3.440.23971440.18861309X-RAY DIFFRACTION99.38
3.44-3.930.22531420.17131310X-RAY DIFFRACTION98.78
3.93-4.950.1881500.14951323X-RAY DIFFRACTION99.19
4.95-44.850.23541570.19241367X-RAY DIFFRACTION99.87
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)
10.1235827746270.0137585518212-0.09361836367280.129007981264-0.1522225226840.237785821090.0478183082343-0.06641248357580.03532430155010.0314347722750.1332982011720.0769280205735-0.0427044085169-0.198019119340.2598351159950.128005328232-0.0798264843410.009933339986240.1655139080650.0360775864072-0.016612971044331.110120990428.105604247768.4949447939
20.007782507100610.03784065295160.04187641919320.2100956495730.2468088541490.314218227018-0.102407144497-0.0291202371861-0.06251447168590.00681754474128-0.194766430656-0.008167509196260.07310138892760.0294376372753-0.07435132784960.255601045584-0.001601909474550.05667249822020.1523533902820.02605756758350.21390857333340.412662828813.372916967365.2114057632
30.1971190894160.08255194910760.01831327851910.1345735613220.129943999750.3222964287070.003980564796080.1628386426280.01576409306380.07990155328630.02398328944840.04049715855650.378359602727-0.1515272970990.03115348635450.0264346670877-0.0692690094556-0.02271949300950.0358868198593-0.01262720922230.065662524885142.774877496823.204469282739.1226253761
40.1287464643120.02488532194280.08993350738670.02774936659540.05156694587680.0925369947607-0.01447286268890.1284826807660.1163185898940.008747173449250.0226077621460.135848376542-0.173506003848-0.015017292785-0.00390017779170.1121624339870.0334515543720.02072047283770.08571907093750.02804137694680.17389151653439.482086581644.063075616738.3883052244
50.132458425762-0.083671605650.05666245237160.0404119488819-0.04010620780610.0406190734170.0722600310150.0447009844560.09607303802060.0656756895358-0.0874977291681-0.0365139504133-0.0004567181189940.0826270977317-0.01135796134130.133415325925-0.04403018508730.01651023057980.121972674394-0.01971448138250.14840730156639.346658053234.391007696262.7615269355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 194 )
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 227 )
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 351 )
4X-RAY DIFFRACTION4chain 'A' and (resid 4 through 53 )
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 97 )

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