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- PDB-7x4g: CD-NTase ClCdnE in complex with substrate UTP -

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Basic information

Entry
Database: PDB / ID: 7x4g
TitleCD-NTase ClCdnE in complex with substrate UTP
ComponentsClCdnE
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 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Cyclic dipyrimidine nucleotide synthase CdnE
Similarity search - Component
Biological speciesCecembia lonarensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: ClCdnE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9054
Polymers35,9121
Non-polymers9933
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-17 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.581, 132.581, 132.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-704-

HOH

31A-706-

HOH

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Components

#1: Protein ClCdnE


Mass: 35911.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cecembia lonarensis (bacteria) / Gene: B879_03742
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: K1KYT0
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MgCl2, ADA, PEG 6000, UTP

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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: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 12099 / % possible obs: 100 % / Redundancy: 22.5 % / Biso Wilson estimate: 41.32 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.017 / Net I/σ(I): 50.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 22.6 % / Rmerge(I) obs: 1.874 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1180 / CC1/2: 0.729 / Rpim(I) all: 0.403 / % possible all: 100

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Processing

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

7x4a


Resolution: 2.6→26 Å / SU ML: 0.2937 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.4105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2011 600 4.98 %
Rwork0.1682 11441 -
obs0.1699 12041 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 0 221 2752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182586
X-RAY DIFFRACTIONf_angle_d0.49683505
X-RAY DIFFRACTIONf_chiral_restr0.0418367
X-RAY DIFFRACTIONf_plane_restr0.0037440
X-RAY DIFFRACTIONf_dihedral_angle_d18.6988955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.860.29881440.24912768X-RAY DIFFRACTION98.31
2.86-3.270.25821480.21012858X-RAY DIFFRACTION99.93
3.27-4.120.19241550.14992860X-RAY DIFFRACTION100
4.12-260.1571530.14172955X-RAY DIFFRACTION99.97
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)
11.978605271840.4139432601240.5737615143411.96486438259-0.6762410680141.357935558370.051183489198-0.09524164707-0.2225927384320.425405668896-0.319193043843-0.651090899253-0.1369373372680.3958820801050.1870472019640.370025681091-0.000158565917248-0.02168448345070.4862636766030.1382665750880.29456389896531.727312191143.520034692463.1764987138
22.881009926370.05680953667171.36720032211.97751414266-0.6030288989351.97042873640.132445570886-0.15358119652-0.361143074557-0.111273930295-0.09270448649190.3190505858070.290633335219-0.0918051448385-0.02817851426790.29449570780.03694752499670.0121650286440.3207537600150.03463962691040.35227467977415.054027353931.179288981753.7869407208
31.76054925798-0.5376244479080.5439495761933.54329772639-0.9874446823282.443944212190.01190797508010.1763036464530.174865574393-0.130574213473-0.350915123787-0.1661122577-0.2162659511890.4995277903980.2628428887620.3018959443530.03921224939810.007585859909430.3923378526230.1034976997830.24670777558426.499079592153.41748614648.3230778709
43.271327421650.2474303665490.8555393418542.736539765031.035965850393.97045608302-0.2079925146590.1231014129570.994854577160.127139272827-0.2365438602810.0988057719307-0.7555433981210.5441100398480.1904005543660.543976307858-0.0651144138782-0.08564568821010.3423222628020.07457318655910.46234992897424.391595677866.908408737552.0589516332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 278 )
4X-RAY DIFFRACTION4chain 'A' and (resid 279 through 298 )

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