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- PDB-7x4t: LpCdnE UMPNPP Mg complex -

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Basic information

Entry
Database: PDB / ID: 7x4t
TitleLpCdnE UMPNPP Mg complex
ComponentsCyclic dipyrimidine nucleotide synthase
KeywordsTRANSFERASE / CD-NTase / cGAS / cyclic dinucleotide / complex / substrate analogue
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 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2KH / Cyclic dipyrimidine nucleotide synthase CdnE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim
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
B: Cyclic dipyrimidine nucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,26114
Polymers69,9222
Non-polymers2,33812
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-29 kcal/mol
Surface area15890 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-20 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.495, 72.910, 66.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-682-

HOH

21B-743-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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

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Non-polymers , 5 types, 554 molecules

#2: Chemical
ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: UMPNPP, MgCl2, Li2SO4, Tris, PEG 3350

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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: 2.2→30 Å / Num. obs: 40378 / % possible obs: 98.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 28.51 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Net I/σ(I): 29.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 3848 / CC1/2: 0.979 / Rpim(I) all: 0.093 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X4F

7x4f


Resolution: 2.2→28.92 Å / SU ML: 0.2031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1973 1958 5 %
Rwork0.1589 37169 -
obs0.1609 39127 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.37 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 137 542 5461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425054
X-RAY DIFFRACTIONf_angle_d0.69586867
X-RAY DIFFRACTIONf_chiral_restr0.0475729
X-RAY DIFFRACTIONf_plane_restr0.005862
X-RAY DIFFRACTIONf_dihedral_angle_d15.51121839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.24281330.17662519X-RAY DIFFRACTION96.05
2.26-2.320.22951350.17232565X-RAY DIFFRACTION97.37
2.32-2.380.23691360.16962587X-RAY DIFFRACTION97.46
2.38-2.460.2281370.1712610X-RAY DIFFRACTION98.18
2.46-2.550.26181390.17442631X-RAY DIFFRACTION99.07
2.55-2.650.22281370.16892617X-RAY DIFFRACTION99.06
2.65-2.770.22151400.16932639X-RAY DIFFRACTION99.46
2.77-2.920.2231400.17062657X-RAY DIFFRACTION99.68
2.92-3.10.21111390.1722670X-RAY DIFFRACTION99.89
3.1-3.340.19751420.16512681X-RAY DIFFRACTION99.79
3.34-3.670.19261420.14772696X-RAY DIFFRACTION99.96
3.67-4.20.1671420.13492701X-RAY DIFFRACTION99.96
4.21-5.290.16041440.1352735X-RAY DIFFRACTION99.86
5.29-28.920.17661520.17462861X-RAY DIFFRACTION99.34
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)
11.62924667496-0.188172058460.8011645953861.22163552288-1.034397000133.46482343826-0.09973980800290.3121837000650.0200963694663-0.217112051328-0.297738189774-0.1865193325680.3090633184990.3063325430920.1497277507190.3916892478140.1178632076050.02387349588210.3544634220170.03156344619240.26330073120354.45362788457.7680495540651.7372727322
23.19618215165-2.414714283272.348336467274.10492098341-2.80401851663.970256287520.246158183799-0.0944106040820.0961580496868-0.0986862888581-0.313588636488-0.3105858229540.1169719806330.9610303315470.1320888471010.399614022587-0.02211168255690.09322407253880.439911550563-0.02375508368280.2456487965844.80488817523.977529244730.1709838328
31.12035080738-0.5313439292140.3282931453571.85367726557-0.6832549396841.558428641060.02547370318470.101466586030.0944499219959-0.2766144801140.0337680188348-0.0890303726505-0.224124464690.0803214216583-0.01537295487620.379861250722-0.01033274309240.03161595761230.2043846375270.02164991948130.13621025444440.023449124831.182094713333.2254203599
41.11727143272-0.4196641712930.250928809431.301106216990.1142848248281.222300488680.1010059443490.0416924286586-0.0772704125582-0.179557873395-0.1296429114510.20066122644-0.0007426414493050.1508925404960.02537700389570.308741701741-0.02227500628060.01357925629610.203714820031-0.001781774969140.15804777341939.575606613726.643761601241.2477870223
50.7881197728060.3255643713290.806591423350.361452666625-0.02895293902871.379038914220.038043887219-0.07926828390350.148617104265-0.0767259354134-0.1474770812570.244454723983-0.230545618048-0.530911552861-0.04081399741060.3274539668270.06242215744340.02552341117890.251784343890.003820258327660.25695485722827.838513688438.028755600437.4108292535
60.396736811330.2563890626850.2044801308140.8993135799130.3142045447710.7032959036320.02211286173070.0956899729152-0.0804632437707-0.08020545712230.031799351073-0.05379622228130.123268252914-0.0107014470482-0.05001316499860.342826766605-0.009311255308760.004905863849440.213453093439-0.009937908953140.15954388446334.101450052224.27960452835.6612466338
71.275990939850.04487226381930.1666938505560.5914855994070.2128379503891.392126836440.0797265732583-0.1755544379050.2309359661420.0662422704449-0.07426516608710.114717717168-0.253686799742-0.0459204607505-0.02817771089980.312732037892-0.004998901139950.03541318429640.190983722816-0.01544779701030.17552131629535.411115589440.270747733148.0855342705
80.425425044436-0.1592705881150.0001404960895791.35356012101-0.575914222171.372512369490.01189978113670.00336547795882-0.03192001787280.188106709671-0.0905532433618-0.0226482653014-0.02341635447930.1232429596050.07124913238680.282920420692-0.01531031219870.003075387276740.2173336552320.01649388913140.13449064483446.558955824320.966965154658.0422108775
90.24125903434-0.2515927855250.4025480720942.23507253163-1.570236982941.53598774828-0.104272410419-0.0106780185999-0.1869993240820.1910378860070.005318646535950.07739892079690.3619370024390.0493986026940.03316273247830.417028319607-0.008615497010940.07517267454370.2628949814220.02976112319160.21281565992541.76480084388.2838679140368.5280235412
103.05196911767-1.28922279442-1.523783678730.7659429786190.4404575550740.889272925463-0.141106516253-0.6106968070730.3044845433760.1116192584970.3615436515150.216959534499-0.2072158260310.0703985066548-0.09666313019170.30205714650.1107233486360.03477759052570.446354695068-0.01992714141710.42200709664212.158217546416.164557514544.2750747944
111.36171436466-0.59241204685-0.3405063618771.193202308380.254175268830.558293554459-0.0383590930781-0.03860340660640.122292169834-0.1701920432810.05452764270410.281390268590.0421266785475-0.102388439544-0.0002760869373860.1870663579590.0136349685019-0.0503364455470.2096774226210.009273495492310.27488973868417.795938100112.20759624929.0196389538
120.000589179232484-0.05192960610040.02377243749561.85437618161-0.6410985720350.2225425870710.2381179896150.7193334164440.233247000469-0.669181011377-0.252165720546-0.216190443171-0.0340543782672-0.1779271815490.01034072498160.7568536400690.229631118851-0.134883486460.7550141379170.107355768410.28331390134814.751311009815.12888917945.43947246014
131.89349648603-0.30960367251-0.09562341984811.608280153980.03189906753421.00761238143-0.108168035896-0.0401805475949-0.183429234872-0.1010094096130.06808876396350.1482274880180.0324618267373-0.1133227501350.0640352261490.1729872915220.0239740605968-0.03145782675070.203235702042-0.005734134955690.23395901993619.02120513293.261201352228.3922637228
141.0616272832-0.247419461197-0.231349065021.495808026580.2958407796490.7233085895070.05457617028050.2094339197130.324963911295-0.3920485982920.03547865113650.129027889454-0.0788458751924-0.0113395511386-0.1257070271180.283419434110.00944670635221-0.1354872686170.3037324983710.06054131639590.4588463875799.8106347492320.704789504522.1391954023
151.35451722299-0.2378215991960.09182490595640.6816401974520.1294681966040.62216334201-0.0317251794403-0.335107497882-0.04480739227280.214297819330.2536036181220.547921250670.0426499144819-0.0960143552148-0.09028172182580.1449205667790.0387953227486-0.02188858306740.3472569383260.09702787066660.648409999221-4.9217737098120.058421912239.576664471
162.101987500440.35187892579-0.101342743690.0616582358060.004416121260730.4781674817640.07668374308350.331204142563-0.0352287966978-0.4091783910380.1036557140830.5074833916860.221431976594-0.215190627634-0.03292258045620.324812799322-0.00276845904499-0.2282707752880.354162981610.06624696585610.606960055837-3.9061951038717.654691009623.878184074
170.989796416054-0.3260155956590.5387190366130.267253061857-0.04589718158540.725891681528-0.0716310007019-0.435114712980.07718417446780.02060700289410.2004156136940.3012149465120.0171876012634-0.3118946497740.2246214986050.07349596534080.0394447651006-0.08138664623780.4177896508310.1329756689840.928034455361-13.787358422214.497902006239.9047015039
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 19 )AA3 - 191 - 17
22chain 'A' and (resid 20 through 36 )AA20 - 3618 - 34
33chain 'A' and (resid 37 through 56 )AA37 - 5635 - 54
44chain 'A' and (resid 57 through 79 )AA57 - 7955 - 77
55chain 'A' and (resid 80 through 115 )AA80 - 11578 - 111
66chain 'A' and (resid 116 through 149 )AA116 - 149112 - 145
77chain 'A' and (resid 150 through 174 )AA150 - 174146 - 170
88chain 'A' and (resid 175 through 277 )AA175 - 277171 - 273
99chain 'A' and (resid 278 through 302 )AA278 - 302274 - 298
1010chain 'B' and (resid 4 through 36 )BG4 - 361 - 33
1111chain 'B' and (resid 37 through 79 )BG37 - 7934 - 76
1212chain 'B' and (resid 80 through 99 )BG80 - 9977 - 96
1313chain 'B' and (resid 100 through 149 )BG100 - 14997 - 146
1414chain 'B' and (resid 150 through 191 )BG150 - 191147 - 188
1515chain 'B' and (resid 192 through 254 )BG192 - 254189 - 251
1616chain 'B' and (resid 255 through 277 )BG255 - 277252 - 274
1717chain 'B' and (resid 278 through 295 )BG278 - 295275 - 292

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