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- PDB-7ljl: Structure of the Enterobacter cloacae CD-NTase CdnD in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7ljl
TitleStructure of the Enterobacter cloacae CD-NTase CdnD in complex with ATP
ComponentsCyclic AMP-AMP-GMP synthase
KeywordsTRANSFERASE / CD-NTase / CBASS / trinucleotide
Function / homology
Function and homology information


nucleotide metabolic process / nucleotidyltransferase activity / 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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cyclic AMP-AMP-GMP synthase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGovande, A. / Lowey, B. / Eaglesham, J.B. / Whiteley, A.W. / Kranzusch, P.J.
CitationJournal: Cell Rep / Year: 2021
Title: Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense.
Authors: Govande, A.A. / Duncan-Lowey, B. / Eaglesham, J.B. / Whiteley, A.T. / Kranzusch, P.J.
History
DepositionJan 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic AMP-AMP-GMP synthase
B: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,38520
Polymers86,7892
Non-polymers2,59618
Water14,520806
1
A: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,69210
Polymers43,3951
Non-polymers1,2989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,69210
Polymers43,3951
Non-polymers1,2989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.074, 101.372, 68.364
Angle α, β, γ (deg.)90.000, 117.611, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cyclic AMP-AMP-GMP synthase / cGAS/DncV-like nucleotidyltransferase / CD-NTase038


Mass: 43394.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: cdnD02, P853_02262 / Production host: Escherichia coli (E. coli)
References: UniProt: P0DSP4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 6.5, 19 to 21% PEG-1000, MgCl2, ATP

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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: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→38.87 Å / Num. obs: 140248 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 19.75 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 13.8
Reflection shellResolution: 1.45→1.47 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6821 / CC1/2: 0.619 / Rpim(I) all: 0.558

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model of the selenomethionine substituted protein, determined using SAD phasing

Resolution: 1.45→38.87 Å / SU ML: 0.1348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1652 2044 1.46 %
Rwork0.152 138050 -
obs0.1522 140094 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.6 Å2
Refinement stepCycle: LAST / Resolution: 1.45→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5615 0 156 806 6577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795910
X-RAY DIFFRACTIONf_angle_d1.04228045
X-RAY DIFFRACTIONf_chiral_restr0.0719852
X-RAY DIFFRACTIONf_plane_restr0.00641020
X-RAY DIFFRACTIONf_dihedral_angle_d18.55932197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.25921380.25828964X-RAY DIFFRACTION97.63
1.48-1.520.24381290.22819246X-RAY DIFFRACTION99.69
1.52-1.560.22771300.2059182X-RAY DIFFRACTION99.67
1.56-1.610.22881420.19399195X-RAY DIFFRACTION99.67
1.61-1.660.20791270.1869230X-RAY DIFFRACTION99.61
1.66-1.720.20971320.17639149X-RAY DIFFRACTION99.3
1.72-1.790.19771400.16919248X-RAY DIFFRACTION99.8
1.79-1.870.18631440.16019194X-RAY DIFFRACTION99.94
1.87-1.970.17391310.15199240X-RAY DIFFRACTION99.79
1.97-2.090.1741310.14669221X-RAY DIFFRACTION99.57
2.09-2.250.14921430.1419179X-RAY DIFFRACTION99.21
2.25-2.480.14221410.13469132X-RAY DIFFRACTION98.57
2.48-2.840.15351340.13829293X-RAY DIFFRACTION99.94
2.84-3.570.13651390.1469283X-RAY DIFFRACTION99.92
3.57-38.870.16611430.14679294X-RAY DIFFRACTION98.78
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)
10.4803209274960.21395948639-0.09423022012680.2479521514430.09363985694670.182431706374-0.06836899259110.1326922373130.122798166221-0.03830686584680.030518834082-0.294371706230.05823612212180.150792203401-6.44486714367E-50.1765232861470.03044986985870.01892790385110.271922012645-0.02130168840730.20251050788531.87703726430.75517770399.30539350582
21.06574314558-0.02522255567020.3117226765820.15706114765-0.1233296742790.8676734802550.01651396863240.2695525966770.0254120388021-0.0454467614444-0.02509317989360.0257767674555-0.02685405585560.0467592915361-7.32740249443E-50.172572825242-0.001437322526050.001045803525420.206726831646-0.00196399667130.16683579255214.657473660639.82650892436.12499466543
30.70465304375-0.2315871798070.08990677918150.634002991153-0.1550843714010.828185171763-0.02876699485360.001031699923480.01457618921760.03574264290410.0280830839879-0.02792670170580.0218025908270.06463342231424.82033369613E-60.15752167966-0.0008500124436710.0002788429268040.145548528515-0.0200260321760.16080693837621.319829939832.001358192822.7893373517
40.1951059092720.1872574650060.02562029149360.443622220461-0.02857354631060.613460003512-0.1871552626690.0590089029354-0.417537497348-0.006663051019650.0823262726822-0.01485200288460.4564675287890.156294803038-0.0151195249320.3182199385220.09454528895450.02620468716040.187831659239-0.004318226750560.27292659381430.21825393229.0466263326821.6711033949
50.0518375147580.0873669805719-0.119396167820.223649425255-0.1376299848160.739892347089-0.0342293160792-0.3582568440340.1893869721470.4509073864820.08492159894890.3112976345910.0732898584165-0.3733741760940.1444479313690.3215540620570.1320447271970.03688543543710.339384381889-0.07339703152230.28731086956441.984356840657.671306898510.9808250471
60.7069616296950.05026434119930.2153032483030.4919586018040.3259908046350.9547917949820.03949721968130.0814604547155-0.03047628103130.00841644836715-0.0505731341620.02166320782430.0530466616321-0.2656808431092.49972364197E-50.1726210632770.00579302814130.002869613222390.2622159617880.01801603905340.15894177833444.47220335235.9983006764-12.2826718733
70.1845768713390.1699496574750.1343837520860.1350043396470.09419494365740.211549336840.01549067767-0.0610848911986-0.1801857135110.221057937944-0.005272150907210.003975980878970.242891153604-0.161011272775-0.0001652739226540.250513337944-0.0121367419362-0.00252361434950.2398504764620.04721811333920.24666678862450.732296770428.78787276210.166627633871
80.2026383087740.06566506874910.1305493602240.1308746676060.0008580485315520.169581407002-0.0958087907587-0.611851627149-0.09970059257990.3074830022360.0511396746812-0.05510375338810.163232291172-0.0964100171528-0.02217171069630.3159884304680.01744563907570.01072605989640.3301543459050.0893793443380.21732234354752.521084691930.63120287959.26460426913
90.440963813636-0.0226700266720.2139014298540.453200282850.2557813334360.2574573829990.003909690546980.01169506531280.02543364855710.003152374929520.0933244620179-0.068529747355-0.04587614935520.06728053304167.85201884588E-50.1760157438870.01343223080760.00392932764540.1725806354750.01850549925590.1594218373558.596617303538.9204272659-3.24992055098
100.8167816047340.314316208583-0.09797318799480.544864154387-0.007512671338730.548975244253-0.0904511723935-0.02434291434830.194167499370.02853703145580.08616184159610.0536360231842-0.126324515215-0.008558187572955.74599155885E-60.2079950265420.0249273226289-0.02473065198030.1593615827940.01603864805890.21996820591859.08351903155.64258213990.787543407355
110.8859344774510.08958199381310.4293079968350.2330608930240.2377211129280.398929490903-0.1173569283320.07338228157170.610477433403-0.08834774067610.0916307046610.0746039356968-0.3922109941010.0563468656169-0.186890393360.2992490072390.0152647899275-0.0639141477140.13020215572-0.01082683403950.36898116783859.363495211766.14421664142.40575011446
120.05025725227060.02191601205270.06251715557580.0235205692383-0.04296052796820.8113135708810.0530821808755-0.1394221062750.3047025958440.03776023364960.04370293107590.109470640254-0.160156031646-0.3668833850750.2678169384220.3130278014570.154722156357-0.0265368299870.25399222293-0.1042588633960.58137392848642.582160487468.933752151112.4869201914
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 37 )AA0 - 371 - 38
22chain 'A' and (resid 38 through 117 )AA38 - 11739 - 118
33chain 'A' and (resid 118 through 309 )AA118 - 309119 - 302
44chain 'A' and (resid 310 through 354 )AA310 - 354303 - 347
55chain 'B' and (resid 0 through 17 )BB0 - 171 - 18
66chain 'B' and (resid 18 through 130 )BB18 - 13019 - 131
77chain 'B' and (resid 131 through 154 )BB131 - 154132 - 155
88chain 'B' and (resid 155 through 186 )BB155 - 186156 - 176
99chain 'B' and (resid 187 through 223 )BB187 - 223177 - 213
1010chain 'B' and (resid 224 through 309 )BB224 - 309214 - 299
1111chain 'B' and (resid 310 through 332 )BB310 - 332300 - 322
1212chain 'B' and (resid 333 through 364 )BB333 - 364323 - 348

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