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- PDB-7x4q: LpCdnE UTP Mg complex -

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Basic information

Entry
Database: PDB / ID: 7x4q
TitleLpCdnE UTP Mg complex
ComponentsCyclic dipyrimidine nucleotide synthase
KeywordsTRANSFERASE / CD-NTase / cGAS / cyclic dinucleotide / substrate complex
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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Cyclic dipyrimidine nucleotide synthase CdnE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / 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 / _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
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)71,95610
Polymers69,9222
Non-polymers2,0348
Water10,647591
1
A: Cyclic dipyrimidine nucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9785
Polymers34,9611
Non-polymers1,0174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-28 kcal/mol
Surface area14780 Å2
MethodPISA
2
B: Cyclic dipyrimidine nucleotide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9785
Polymers34,9611
Non-polymers1,0174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-26 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.584, 74.719, 80.343
Angle α, β, γ (deg.)90.000, 98.227, 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
11ILEILEASNASN(chain 'A' and (resid 3 through 116 or resid 118...AA3 - 873 - 87
12SERSERPHEPHE(chain 'A' and (resid 3 through 116 or resid 118...AA97 - 11597 - 115
13LEULEUTHRTHR(chain 'A' and (resid 3 through 116 or resid 118...AA118 - 161118 - 161
14ILEILEHISHIS(chain 'A' and (resid 3 through 116 or resid 118...AA163 - 300163 - 300
15UTPUTPUTPUTP(chain 'A' and (resid 3 through 116 or resid 118...AC401
26ILEILEASNASN(chain 'B' and (resid 3 through 87 or resid 91...BB3 - 873 - 87
27SERSERPHEPHE(chain 'B' and (resid 3 through 87 or resid 91...BB97 - 11597 - 115
28LEULEUTHRTHR(chain 'B' and (resid 3 through 87 or resid 91...BB118 - 161118 - 161
29ILEILEHISHIS(chain 'B' and (resid 3 through 87 or resid 91...BB163 - 300163 - 300
210UTPUTPUTPUTP(chain 'B' and (resid 3 through 87 or resid 91...BG401

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Components

#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
#2: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: UTP, MgCl2, PEG 4000, ammonium acetate, sodium citrate

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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: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 56124 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.04 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.044 / Net I/σ(I): 17.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5577 / CC1/2: 0.857 / Rpim(I) all: 0.306 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X4F

7x4f


Resolution: 1.95→27.23 Å / SU ML: 0.1775 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 2700 5.1 %
Rwork0.1614 50248 -
obs0.1627 52948 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.67 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 0 591 5451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724983
X-RAY DIFFRACTIONf_angle_d0.88066775
X-RAY DIFFRACTIONf_chiral_restr0.0553721
X-RAY DIFFRACTIONf_plane_restr0.0056849
X-RAY DIFFRACTIONf_dihedral_angle_d23.75461801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.25971090.21261878X-RAY DIFFRACTION67.7
1.98-2.020.22111200.19832057X-RAY DIFFRACTION73.67
2.02-2.060.21921140.19832239X-RAY DIFFRACTION79.82
2.06-2.110.25531280.2022374X-RAY DIFFRACTION85.48
2.11-2.160.2621320.18992534X-RAY DIFFRACTION91.46
2.16-2.210.21621600.18082684X-RAY DIFFRACTION96.15
2.21-2.270.23031250.18272768X-RAY DIFFRACTION98.37
2.27-2.340.19151600.17262785X-RAY DIFFRACTION99.59
2.34-2.410.19051590.1642757X-RAY DIFFRACTION99.93
2.41-2.50.22021450.1632804X-RAY DIFFRACTION99.97
2.5-2.60.18381430.17182806X-RAY DIFFRACTION100
2.6-2.720.20221600.16032767X-RAY DIFFRACTION100
2.72-2.860.18391420.16282831X-RAY DIFFRACTION100
2.86-3.040.18521460.15692801X-RAY DIFFRACTION100
3.04-3.280.17621650.1572801X-RAY DIFFRACTION100
3.28-3.60.16681560.15022800X-RAY DIFFRACTION100
3.6-4.120.17361410.14032845X-RAY DIFFRACTION99.93
4.12-5.190.13671570.13082811X-RAY DIFFRACTION100
5.19-27.230.17961380.16812906X-RAY DIFFRACTION99.71
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)
10.0253727732482-0.0103606345405-0.0153923940670.00419146354390.006208310751310.01194419176180.001469512025-0.01050220752720.03768325651550.0170922641466-0.0170822045596-0.00757879126422-0.0424923839205-0.0227834859780.002238303559950.271199114426-0.0292267531683-0.05769420428410.205781904959-0.1195798357120.29851361715818.949946394617.078074483715.3138319242
20.00400448028357-0.003585930685930.001498752267770.00381278717003-0.0006317074284130.0003297252166640.00950817993753-0.087068160245-0.01571307342020.006417555717420.02728672664610.05174321696860.01861562805960.02570638469819.73290473941E-60.1087915017820.04557247394170.02157882474260.271357672423-0.02193726297650.21451309029-2.971972798521.109808355685.19013459034
30.09238475294630.0118864552602-0.02834851770310.05432756558990.02684625033670.0494253533732-0.00728314594304-0.0831366474818-0.01474920134620.01042329697410.02011565281170.1259628976970.01332419471940.01005754044140.05536131440930.07109856219340.018378178469-0.03755049242030.0822013398878-0.005741572804330.1395109141054.21372005881-4.044981991570.282128180372
40.01236971210030.0173443178542-0.008688519450180.0232185038119-0.01847284207510.0239799594764-0.03343204563610.0782672921679-0.0316972235479-0.09538762424270.05382628434880.01244449988380.0595883937576-0.00809322531814-0.008335036478590.1724710140320.0354336185342-0.05176951654360.122204407705-0.03033060510.1526270023323.96208459171-10.6956887059-10.3761028837
50.03972539684310.0476790717940.01273654567370.05242796071620.02109152471590.08404287900570.02180387191030.0006769061619180.00482483667025-0.0208499874722-0.07803741912790.04316627710070.0405163882791-0.048723904786-0.07322672565540.03856416495730.0882506401928-0.05547153907680.06707143881590.01811172274760.06179530614598.01517045416-6.53007889645-4.90389366848
60.01287099517520.01010611387340.0130548710560.0236865917050.0259008989310.02905119017070.0189991851247-0.08887212188690.1250987444010.0769471243024-0.0862882092313-0.040471310902-0.034655574731-0.0376342226642-0.0247840889790.0524801694945-0.116552940436-0.0742539050740.0484826829431-0.006724364162950.11126931718524.21501941765.817993198719.68765459136
70.005918054886148.51824043593E-5-0.001728189798030.002819513689070.002213318759760.00320019341480.02680371112990.0520802184765-0.0232834060603-0.01546279960750.0216802327721-0.0719686772107-0.0063705583204-9.2810387919E-50.006412891688680.0916748244508-0.0220892508878-0.002466932775960.1045609065490.01780573200770.10357528516727.0703127127-3.90350028116-1.20651241012
80.003222108635830.00248385061747-0.00620501224590.00361397366504-0.003406765513410.0106244008725-0.0389347873602-0.06485544516910.0733269593004-0.002275658558780.0137380250189-0.0448219907991-0.07238861164360.02852204872820.0004541224339450.160865521802-0.0726786130601-0.02886305122560.1366506316490.01307168239840.24549434609534.726456523916.35760837153.07953471272
90.07471932296940.006685059728170.0300410508930.02618833829640.0004385550996450.0156657820001-0.08426262875710.132056687870.0546000251125-0.07795469191560.07801564199260.101413130197-0.07978488413740.0192054587425-0.005067579296560.111123578189-0.0212183473766-0.01822663725040.1573411265290.03892476804570.1234608850783.89487266344-14.589547139315.2077437904
100.1582551811450.0604573118461-0.06325833007320.0477210200099-0.08988882257420.20662313367-0.128046306060.0678032131804-0.107172474604-0.0574659120867-0.0310980172965-0.1027622535480.1011243296590.032535047972-0.1929999426490.11031706125-0.03806030245080.05970760069950.06775401145520.009617112254030.11752253515914.2429554755-27.836283266519.4916551953
110.0148105611483-0.01439145953950.02129433022240.03044743312090.004072317581570.0639477472026-0.0887540308496-0.0475154610687-0.06341859912770.09644763687430.02625031420920.01041857933620.08783169188270.105473644713-0.03443411396690.150333939990.06340989962770.05496135391380.1808210698720.1314450823890.20021847076620.7348919341-37.130926721827.0928368782
120.079177626368-0.0671554895019-0.1193509745770.05439178943520.1001637219490.185645819951-0.113831923989-0.0568634420371-0.05822550337160.0287253592806-0.0498538974334-0.01913743583460.05175690139070.100877712328-0.1253529369370.109211890145-0.0189374680968-0.0125859598340.155108540770.06827582339010.1154307391319.7726806566-23.379483740622.1526852937
130.124761693423-0.0733162475339-0.09212750201260.04452467107960.05298496660630.0761560206071-0.0840963329623-0.00953448144195-0.114784676328-0.00856097546345-0.0538506525658-0.003970323965040.1469960313390.0688732082815-0.09619332187490.2646791774190.01970224661950.101616011610.1127858883650.08880361469490.14003955398510.1761663675-38.891792683229.8243862822
140.107490826113-0.03390913014190.00360817259170.095556208232-0.02655117818030.014808382466-0.0743362966150.08252009067070.01408301728530.119102985832-0.01483486749380.1426935871060.0639896785694-0.082564351552-0.07969838263870.128896987505-0.03068061562120.04228690448070.127992982792-0.0533561686090.143821410792-6.4353868184-17.746055930627.2153460486
150.01681759658930.0001644571540010.01420614324070.03531012807560.01146916953570.0167964671922-0.0204242435157-0.0284981825731-0.01549475617360.0901684985193-0.005971155670530.02735946922360.0210973545773-0.020435198449-0.07060187887650.26677421048-0.01452397043980.1552418145460.10771871064-0.00924052823510.0675456554426-0.588525397382-27.38830530436.9295824415
160.065671447260.01427094940960.04803329948020.003702275048090.009254126801510.0528332317016-0.00133208033821-0.02061581019190.07254155541130.000674910945609-0.05245728333130.0605109691009-0.0426871789677-0.07010217725-0.01802668299060.2608004410850.02160451480790.106103067930.154514066746-0.07327805207520.195099651298-9.3349951701-7.2272519004539.0326190795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 254 )
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 277 )
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 300 )
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 36 )
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 79 )
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 115 )
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 149 )
13X-RAY DIFFRACTION13chain 'B' and (resid 150 through 174 )
14X-RAY DIFFRACTION14chain 'B' and (resid 175 through 254 )
15X-RAY DIFFRACTION15chain 'B' and (resid 255 through 277 )
16X-RAY DIFFRACTION16chain 'B' and (resid 278 through 300 )

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