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- PDB-7d4o: cyclic trinucleotide synthase CdnD in complex with ATP and ADP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7d4o
Titlecyclic trinucleotide synthase CdnD in complex with ATP and ADP
ComponentsCyclic AMP-AMP-GMP synthase
KeywordsTRANSFERASE / cyclic trinucleotide synthesis nucleotidyl transferase
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'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Cyclic AMP-AMP-GMP synthase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsYang, C.-S. / Hou, M.-H. / Tsai, C.-L. / Wang, Y.-C. / Ko, T.-P. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase.
Authors: Ko, T.P. / Wang, Y.C. / Tsai, C.L. / Yang, C.S. / Hou, M.H. / Chen, Y.
History
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)91,50920
Polymers88,7572
Non-polymers2,75118
Water16,844935
1
A: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,84611
Polymers44,3791
Non-polymers1,46810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area15810 Å2
MethodPISA
2
B: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6629
Polymers44,3791
Non-polymers1,2848
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.773, 107.182, 65.875
Angle α, β, γ (deg.)90.000, 118.292, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain 'A' and (resid 1 through 83 or resid 85...AA1 - 831 - 83
12PROPROLEULEU(chain 'A' and (resid 1 through 83 or resid 85...AA85 - 12285 - 122
13ILEILEASNASN(chain 'A' and (resid 1 through 83 or resid 85...AA124 - 150124 - 150
14LEULEULYSLYS(chain 'A' and (resid 1 through 83 or resid 85...AA152 - 162152 - 162
15TRPTRPTHRTHR(chain 'A' and (resid 1 through 83 or resid 85...AA164 - 168164 - 168
16GLNGLNSERSER(chain 'A' and (resid 1 through 83 or resid 85...AA178 - 266178 - 266
17ALAALATYRTYR(chain 'A' and (resid 1 through 83 or resid 85...AA268 - 286268 - 286
18GLNGLNILEILE(chain 'A' and (resid 1 through 83 or resid 85...AA288 - 320288 - 320
19ALAALAPROPRO(chain 'A' and (resid 1 through 83 or resid 85...AA323 - 354323 - 354
110ATPATPADPADP(chain 'A' and (resid 1 through 83 or resid 85...AC - D401 - 402
111HOHHOHHOHHOH(chain 'A' and (resid 1 through 83 or resid 85...AU601 - 604
21METMETMETMET(chain 'B' and (resid 1 through 83 or resid 85...BB1 - 831 - 83
22PROPROLEULEU(chain 'B' and (resid 1 through 83 or resid 85...BB85 - 12285 - 122
23ILEILEASNASN(chain 'B' and (resid 1 through 83 or resid 85...BB124 - 150124 - 150
24LEULEULYSLYS(chain 'B' and (resid 1 through 83 or resid 85...BB152 - 162152 - 162
25TRPTRPTHRTHR(chain 'B' and (resid 1 through 83 or resid 85...BB164 - 168164 - 168
26GLNGLNSERSER(chain 'B' and (resid 1 through 83 or resid 85...BB178 - 266178 - 266
27ALAALATYRTYR(chain 'B' and (resid 1 through 83 or resid 85...BB268 - 286268 - 286
28GLNGLNILEILE(chain 'B' and (resid 1 through 83 or resid 85...BB288 - 320288 - 320
29ALAALAPROPRO(chain 'B' and (resid 1 through 83 or resid 85...BB323 - 354323 - 354
210ATPATPADPADP(chain 'B' and (resid 1 through 83 or resid 85...BM - N401 - 402
211HOHHOHHOHHOH(chain 'B' and (resid 1 through 83 or resid 85...BV601 - 604

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 44378.641 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DSP4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 5 types, 953 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5 mM ATP, 10 mM GTP and 10 mM MgCl2, 0.2 M ammonium sulfate, 0.1 M Na-acetate, pH 4.6, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. obs: 66128 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.63 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.026 / Net I/σ(I): 29
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 8.5 / Num. unique obs: 6346 / CC1/2: 0.974 / Rpim(I) all: 0.093 / % possible all: 95.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data processing
CNSphasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 7D48

7d48


Resolution: 1.87→29 Å / SU ML: 0.1431 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.4228 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1632 2021 3.06 %
Rwork0.1356 64076 -
obs0.1365 66097 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.27 Å2
Refinement stepCycle: LAST / Resolution: 1.87→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5602 0 170 935 6707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125929
X-RAY DIFFRACTIONf_angle_d1.21588063
X-RAY DIFFRACTIONf_chiral_restr0.0778854
X-RAY DIFFRACTIONf_plane_restr0.00731020
X-RAY DIFFRACTIONf_dihedral_angle_d19.75563535
LS refinement shellResolution: 1.87→1.92 Å
RfactorNum. reflection% reflection
Rfree0.2109 136 -
Rwork0.1597 4380 -
obs--96.23 %
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)
10.506961730499-0.08646251441690.004798022545650.1072357317250.04037988162560.44062993224-0.101942798265-0.0998641398857-0.1070449204930.0850399300404-0.0272334521679-0.338406618276-0.06947078235410.131683729761-0.1108286238280.142199415405-0.00847493549424-0.04914690905520.1803692262050.0003157140951040.14694285834116.32415169281.2363475560318.7076179396
20.1801301498150.002945726606930.1010193930710.0559912565960.07913861527880.113126323175-0.0375553698025-0.086280673859-0.1471541303860.0573779840909-0.0429423886627-0.1638799817370.09024232579480.135718236985-5.46907917803E-50.1494912397420.02515235662860.002459173155350.133500637720.01655241939470.1386302329424.77080851109-14.729108279518.3171349238
30.247810977049-0.205157509214-0.1885243986120.233083990404-0.1391820493490.337786845363-0.0517262313701-0.0751425921655-0.02979341529170.0678248492780.0145615914149-0.0666282093267-0.01830617687970.0207751162552-0.02796375170880.140141234860.0196429359574-0.01280061411950.134645853385-0.01234315179790.1084555899321.46728020976-5.8606069006717.8671562553
40.154773540293-0.0508857434685-0.002276955472290.288538861858-0.09005417800930.189108182015-0.103711375608-0.1627096533190.003199140481970.1307780547350.0308645084860.0987263881939-0.02551515800970.0119798930046-0.01785209548010.1697710809820.01483309518510.01079680857420.1951600008830.006430978718520.111183527325-2.37367213019-9.6731877654227.4183668632
50.1197775908330.0905506342687-0.1129666272060.151210402198-0.1766468115870.150403104272-0.0140575770416-0.0499223226463-0.06752068162880.0245926133905-0.0107703947425-0.0006812062226610.167467885654-0.0431152216352-0.0008065928250530.1449101044060.0003596529154140.00852306678740.132434370724-0.01041867192070.1365189760841.75397016738-16.628692267911.1907110524
60.00256799992115-0.0213178070029-0.01052777380050.05246637561310.002142081124990.0754014494339-0.0203474452455-0.0997840532071-0.1156222206060.0268611588396-0.0188005739901-0.2689153236110.001463744386920.2963254879154.48787990945E-60.1476721089640.0133631186616-0.008458694358010.1942389531190.002316109531440.16745616558816.3683753096-10.96412509829.2768774906
70.0193573979875-0.0150267764201-0.02227838721210.1272627844950.06479449045850.109034528089-0.0860921030089-0.02485247084050.004715836369520.01339793841130.0358406467675-0.1405618253650.1460296580110.06406760010771.22514251168E-50.1488323660950.02747305834890.0001717374747880.175448494481-0.007323668433480.16371428451212.8631192538-14.10470929771.20101536446
80.00272469303625-0.0043963629125-0.07103813716970.279667713386-0.06125433271940.0452362966373-0.02865021152620.09426357524940.01691543820060.03273910328820.04218645308070.002948978678480.00254604795905-0.05450041737365.57193921588E-70.1095400156080.00413353246781-0.00093588471170.1270783278420.006339977876260.1179937460670.724501319347-5.985665250176.61503014614
90.4556086410030.203955910375-0.03151960684280.704651374801-0.204806386350.6322997054390.03066331125180.009605830045730.04394369142930.06223739302820.006510172406910.0297422190015-0.134888622314-0.03852516544560.004528747469350.1304299313310.007381661522290.004331849733150.0966485409331-0.003951559621610.1016911651193.7774649213312.65656224072.82986334891
100.0927383443142-0.006655678548470.03428695573070.008033792589710.00871143936690.004849633344290.10318004599-0.1757263954320.4044582876660.502077112817-0.130030431194-0.266031839026-0.7133647112250.4127074383560.009842056334170.382969296453-0.135015008638-0.0718239818430.246190772295-0.01423478289920.28987954438119.829409124124.57323216259.97312515362
110.5267072015740.07607554527890.03533954327990.1625701933490.1393734159530.250714639379-0.0424304577312-0.0847692986482-0.1341505278090.209808642515-0.0479636770866-0.3675408425-0.08782379128870.1395475650820.1019954185530.1170777482030.0148441867629-0.03841349796880.172088746838-0.002729756472960.1983758377498.9846836989836.642058983932.3198136273
120.182362344074-0.1465573007480.01071044390050.1110437314180.1025030284860.167212799461-0.0319218010589-0.0326988572130.05520156389240.0427394761722-0.00726642504537-0.244555715513-0.142306397550.1149802193840.01464037259990.138535418245-0.0234842951896-0.001731730214410.135508274418-0.008780714966390.1585979284612.2853321832852.540616554622.9054844067
130.1461402649920.246122571365-0.1573084045690.218630694623-0.0753925034250.349924826647-0.0101311015730.0439906762119-0.0454228043728-0.02057485494710.000654891347957-0.131493554994-0.02985649878260.0473625801103-0.0006090333051560.1122605363960.01138809155180.01428935257670.120895999492-0.01732768730240.1497059503340.12448492145143.685731393120.422887089
140.1732211910090.0847121179222-0.145037787780.151951480339-0.02075879189790.189489465182-0.005103185821940.0948476349207-0.091813998217-0.2245511547570.050837769592-0.113537345448-0.02334307401780.1263024552240.06251736889160.142722638675-0.01568597853510.03518589196480.194258205289-0.01025944354970.1711419003175.9495522974447.477748562511.9293605189
150.1160002856370.151778588448-0.0605378751420.149349645067-0.1532556357920.2015525572510.06364114708010.05085728768090.0884521866593-0.0478939141159-0.00627321574966-0.0440251120818-0.105206398050.06393419705660.001268216954960.1220059557530.002928077422370.003263608475210.118835535444-0.005845351127470.112112549837-5.3336008303754.445868360724.3113746049
160.1038784489610.0464110439268-0.04684841757780.05778423718950.04099555960720.0458090629504-0.0465387205409-0.08253885761490.03240857710280.249184352506-0.00393161444937-0.144940501722-0.1132236682350.186870731938-1.00523125463E-50.1414885118850.00826897588506-0.02116337780680.165217808286-0.003199819297370.1434149818591.1061813546648.808228488637.5768122508
170.0997114354296-0.00571964613916-0.1089842191110.0985451152245-0.010116515730.0874625868710.040697771816-0.0802655152419-0.009820773939080.08883849393940.00219970820395-0.129266734449-0.02378951316550.115764889193-8.69446700318E-50.1710621487710.00284933906269-0.01837232134210.201341742588-0.00509571509270.162686523514-7.2056934035651.829597780939.5578306849
18-0.04119000479790.0840348636298-0.05562107729430.111321450261-0.1246679530110.0496224649808-0.02012255947050.0110498630048-0.0108697744592-0.02053466943170.0313848155203-0.01197922215950.00605290078761-0.13593907835-2.37099735798E-60.114249453108-0.00322771032362-0.003723647643410.124797533321-0.004793853825080.110569901268-9.7075036491343.788358606325.959167734
190.5778621209580.0995612017561-0.0263749561230.764707587751-0.2354665615080.453381953198-0.05898898325810.0411327046183-0.0914218114357-0.06401799942670.0153555868313-0.04496604079860.0994971143556-0.0240538912169-0.002645548136830.1250871795861.29517700533E-50.01779925191270.0970092070193-0.01028405031550.123902865145-11.106740033425.188786520230.6027084576
200.153194036627-0.0164478565724-0.01213264166110.007468454815120.02013338392880.0347618605156-0.0517341963064-0.0827857378336-0.525271038402-0.00351673450975-0.0786390818483-0.4314293545280.4674015380680.289765492674-0.02563618798480.2456796971190.07708568492770.01411486641380.2075056085130.08032123979340.4087329247143.6359337808113.26764527440.0696343527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 117 )
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 191 )
8X-RAY DIFFRACTION8chain 'A' and (resid 192 through 220 )
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 332 )
10X-RAY DIFFRACTION10chain 'A' and (resid 333 through 355 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 37 )
12X-RAY DIFFRACTION12chain 'B' and (resid 38 through 56 )
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 84 )
14X-RAY DIFFRACTION14chain 'B' and (resid 85 through 117 )
15X-RAY DIFFRACTION15chain 'B' and (resid 118 through 141 )
16X-RAY DIFFRACTION16chain 'B' and (resid 142 through 164 )
17X-RAY DIFFRACTION17chain 'B' and (resid 165 through 191 )
18X-RAY DIFFRACTION18chain 'B' and (resid 192 through 220 )
19X-RAY DIFFRACTION19chain 'B' and (resid 221 through 332 )
20X-RAY DIFFRACTION20chain 'B' and (resid 333 through 355 )

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