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- PDB-7x4f: Native CD-NTase LpCdnE -

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Basic information

Entry
Database: PDB / ID: 7x4f
TitleNative CD-NTase LpCdnE
ComponentsCyclic dipyrimidine nucleotide synthase
KeywordsTRANSFERASE / CD-NTase / cGAS / cyclic dinucleotide
Function / homology
Function and homology information


nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / nucleotide binding / metal ion binding
Similarity search - Function
2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Cyclic dipyrimidine nucleotide synthase CdnE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsChen, Y. / Ko, T.P. / Yang, C.S. / Wang, Y.C. / Hou, M.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases.
Authors: Yang, C.S. / Ko, T.P. / Chen, C.J. / Hou, M.H. / Wang, Y.C. / Chen, Y.
History
DepositionMar 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic dipyrimidine nucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6348
Polymers34,9611
Non-polymers6727
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-19 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.507, 60.507, 100.588
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Cyclic dipyrimidine nucleotide synthase / Cyclic CMP-UMP synthase / c-di-UMP synthase / cGAS/DncV-like nucleotidyltransferase / CD-NTase057


Mass: 34961.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: cdnE02
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DSP3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MgCl2, Tris, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 14892 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.54 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.047 / Net I/σ(I): 16.5
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1507 / CC1/2: 0.652 / Rpim(I) all: 0.378 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X4A

7x4a


Resolution: 2.46→28.97 Å / SU ML: 0.2436 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.8948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 689 4.76 %
Rwork0.1913 13777 -
obs0.1928 14466 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.76 Å2
Refinement stepCycle: LAST / Resolution: 2.46→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 35 197 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252441
X-RAY DIFFRACTIONf_angle_d0.48323308
X-RAY DIFFRACTIONf_chiral_restr0.0421353
X-RAY DIFFRACTIONf_plane_restr0.0036419
X-RAY DIFFRACTIONf_dihedral_angle_d21.2076892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.640.28791550.24742478X-RAY DIFFRACTION87.83
2.64-2.910.28861330.24142854X-RAY DIFFRACTION98.68
2.91-3.330.27371200.22392846X-RAY DIFFRACTION99.7
3.33-4.190.20611540.18062750X-RAY DIFFRACTION95.84
4.2-28.970.17111270.15382849X-RAY DIFFRACTION99.4
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)
10.615987564777-0.7646052946490.07280411639751.259912458410.02075505526930.8436512261380.1640593063010.3075935798080.254211978833-0.18098433277-0.0872964698889-0.150984239786-0.31401076817-0.26023199468-0.1107129587490.4776589396490.0732445203520.04257617939190.2864672446690.03379626482390.404208170103-4.6234620385831.9173177507-1.23741596555
21.586203822820.5152963018551.902824241420.5058096666930.02461961529473.308295016740.112655657101-0.4113967723760.4248978710380.2001196549090.1299007129870.0474151530506-0.193531679218-1.08591275216-0.2433049292580.426107502962-0.0002302426182230.05432919068830.5475244618040.07730246739530.383840044751-18.85116964321.767435425222.9496168925
31.256690210330.3626022980260.4091842921151.26571940044-0.6322931531091.135982642090.0854278988268-0.02371468069220.0405584157118-0.08328166747510.06821069099440.2076512153090.0103761599589-0.533011912289-0.1202549868730.3467566357180.06124268461370.03497925756250.359706390513-0.0001811373754640.319133171642-16.181301801527.97454229014.50938805596
42.50747237356-0.720310864906-1.538200606712.188826169850.9699338837442.67812260230.0466423173852-0.07321953366390.04311766196610.07895571628020.053397439369-0.08713007179760.1436939818790.184560369319-0.08801288727090.2956742442480.0373175035762-0.0001245392276160.2017666800260.01611959244710.2632797167377.287656043115.3986233081-2.00912822356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 99 )
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 297 )

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