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- PDB-7ljm: Structure of the Salmonella enterica CD-NTase CdnD in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 7ljm
TitleStructure of the Salmonella enterica CD-NTase CdnD in complex with GTP
ComponentsCD-NTase
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 / metal ion binding
Similarity search - Function
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Probable cyclic AMP-AMP-GMP nucleotide synthase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
Revision 1.4Jun 5, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD-NTase
B: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,92212
Polymers86,6832
Non-polymers2,23910
Water1,63991
1
A: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4616
Polymers43,3421
Non-polymers1,1195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4616
Polymers43,3421
Non-polymers1,1195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.473, 69.781, 88.697
Angle α, β, γ (deg.)90.000, 110.351, 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 CD-NTase


Mass: 43341.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: GNB57_001779 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A728KSL7
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 25% PEG-3000

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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: Aug 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→38.49 Å / Num. obs: 26345 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 47.36 Å2 / CC1/2: 0.985 / Rpim(I) all: 0.135 / Net I/σ(I): 3.5
Reflection shellResolution: 2.6→2.71 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3093 / CC1/2: 0.381 / Rpim(I) all: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EcCdnD

Resolution: 2.6→38.49 Å / SU ML: 0.3939 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 1982 7.69 %
Rwork0.2289 23791 -
obs0.2318 25773 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.39 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 134 91 5806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295865
X-RAY DIFFRACTIONf_angle_d0.65748005
X-RAY DIFFRACTIONf_chiral_restr0.0428847
X-RAY DIFFRACTIONf_plane_restr0.00471019
X-RAY DIFFRACTIONf_dihedral_angle_d20.16782203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.36941080.31911387X-RAY DIFFRACTION79.39
2.66-2.730.34161230.31311579X-RAY DIFFRACTION90.92
2.73-2.820.33281430.30141689X-RAY DIFFRACTION97.92
2.82-2.910.30361460.28311750X-RAY DIFFRACTION99.42
2.91-3.010.33631530.26821722X-RAY DIFFRACTION99.89
3.01-3.130.31371340.27031737X-RAY DIFFRACTION99.63
3.13-3.270.3391500.26441739X-RAY DIFFRACTION99.58
3.27-3.440.30711430.25371716X-RAY DIFFRACTION99.31
3.45-3.660.29111420.25081723X-RAY DIFFRACTION97.29
3.66-3.940.26431490.21721696X-RAY DIFFRACTION98.03
3.94-4.340.23381380.19131759X-RAY DIFFRACTION100
4.34-4.970.21651500.17731752X-RAY DIFFRACTION100
4.97-6.250.251490.22071765X-RAY DIFFRACTION99.64
6.25-38.490.20641540.19361777X-RAY DIFFRACTION98.52
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)
11.947154265880.4137290153790.5066631920931.08483562814-0.4118176941460.7047889050320.1036509426380.0574334482453-0.0366286011379-0.075651236184-0.1226699000710.000831922033574-0.0699563119366-0.0768986395830.0008507301282530.29637560651-0.01234381397720.01581665902150.2710461346650.02588830633540.358388897894-25.4793555662-8.99121255398-38.6799257682
20.407456765516-0.1084489559450.1443658110620.8157515038450.1777000024750.367746088565-0.0314352321566-0.150678895871-0.5082895804150.308258051733-0.007890815625060.2806219054750.350514971262-0.3492389159820.0002050864792740.480965071489-0.0380221616051-0.05853346445860.3902812412260.05889893909680.484437416928-25.3836948341-24.3874915799-28.0535142316
31.896212130040.00139217857497-0.872428756020.191513666884-0.01818342470031.953346776050.139753539955-0.337461115599-0.07139001062460.395488501584-0.200127923013-0.392135111771-0.3251854813010.194726014686-0.02308366903970.481565677959-0.106195401176-0.04255312897380.323130863553-0.0007322663279830.296231935994-18.199975274-2.78171624396-18.2240098056
41.05630457997-0.36609095960.4664765738010.392799798335-0.4190323731290.592500586665-0.0573702606462-0.6072926006340.00942340201241.13739574055-0.1574748983410.342994245299-0.764136244977-0.408790303580.01074488196480.954989485831-0.008549717236470.1330632381040.932629814094-0.1935357130630.600615932339-39.3395124111.59286873851-5.37981279055
52.003553425410.2617448076450.7806043328370.803454304447-0.656194727281.248538643310.0534576730967-0.1033307801240.005648259278030.0506668022446-0.0560178286110.01181853919040.009439924585950.278357326285-0.0003847002869930.2869222134790.02333286329110.03270904592630.291860603986-0.03528005592390.407040835088-52.2104900859-8.63338570492-46.4337448765
60.659310370962-0.1209336863240.2883433153950.0305581943938-0.003447150653142.144775051190.0601577641869-0.390273438886-0.972810196926-0.0685813601258-0.3321577016090.3198180052930.5268818653640.450043756253-0.008184563500570.417723475746-0.0242603247871-0.0003847324427880.381422057816-0.0377737277020.701801176097-60.2841718849-22.4407379544-49.5362134908
73.300563688-0.564988979814-0.1548946160870.343974071091-0.4426105951781.198489923940.1439477987580.830993473704-0.461148432383-0.299561707880.262575733652-0.02925507761330.459318180214-0.07572938008780.05774667914040.6928203280210.00659777749653-0.04627676346640.670356130194-0.197605598371.13685155746-56.6088795939-26.0765129959-59.6350485731
80.9197007306660.192529745612-0.5532650829080.967465041105-0.2817152777671.941637463050.2201926440330.502821307001-0.15193308395-0.211074673546-0.2091844138190.325432050452-0.284638700878-0.2519788823610.2711364557320.4114880541440.0507702858456-0.02779427668990.50364998498-0.03932389009120.396164109835-59.872009402-8.9659712583-60.2323987644
91.15523435806-0.485345940382-0.8420054356830.8887525403970.3934017339341.744878658660.0920814073930.703659919687-0.0209966187068-0.228019159251-0.04194387298470.300595890866-0.328101430426-0.334212717766-0.03757339678340.5624998162110.102299191149-0.04575175704160.6798743556610.1122489454030.362416512539-62.33483645520.693642601311-70.9652391594
100.909474872763-0.5271527885230.7555677829132.454144468831.928486110073.215262082860.901577310450.7580360989950.69972231574-1.05636272541-0.0180053326161-0.691763576395-0.8816217290190.4132943659091.560271751190.810175133176-0.05609337913040.09806051644691.015226965110.1969724901230.642520919323-41.28673294632.93534070643-79.5265835204
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 141 )AA3 - 1411 - 139
22chain 'A' and (resid 142 through 181 )AA142 - 181140 - 175
33chain 'A' and (resid 182 through 332 )AA182 - 332176 - 326
44chain 'A' and (resid 333 through 354 )AA333 - 354327 - 348
55chain 'B' and (resid 4 through 126 )BB4 - 1261 - 123
66chain 'B' and (resid 127 through 154 )BB127 - 154124 - 151
77chain 'B' and (resid 155 through 187 )BB155 - 187152 - 174
88chain 'B' and (resid 188 through 238 )BB188 - 238175 - 225
99chain 'B' and (resid 239 through 330 )BB239 - 330226 - 317
1010chain 'B' and (resid 331 through 354 )BB331 - 354318 - 341

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