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- PDB-7x4p: CD-NTase EfCdnE in complex with intermediate pppUpU -

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Basic information

Entry
Database: PDB / ID: 7x4p
TitleCD-NTase EfCdnE in complex with intermediate pppUpU
ComponentsEfCdnE
KeywordsTRANSFERASE / CD-NTase / cGAS / cyclic dinucleotide / intermediate complex
Function / homologyBeta Polymerase, domain 2 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Alpha Beta / URIDINE-5'-MONOPHOSPHATE / URIDINE 5'-TRIPHOSPHATE
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.value_order / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EfCdnE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5844
Polymers35,7511
Non-polymers8333
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-16 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.332, 56.777, 64.780
Angle α, β, γ (deg.)90.000, 97.242, 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 EfCdnE


Mass: 35751.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NCBI Reference Sequence: WP_010707292.1 / Source: (gene. exp.) Enterococcus faecalis (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: sodium tartrate, PEG 3350, MgCl2, UTP

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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 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 38096 / % possible obs: 96.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 11.19 Å2 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.021 / Net I/σ(I): 33.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 18.9 / Num. unique obs: 3716 / CC1/2: 0.993 / Rpim(I) all: 0.04 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X4C

7x4c


Resolution: 1.6→27.96 Å / SU ML: 0.1461 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.8663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1884 1908 5.01 %
Rwork0.1487 55515 -
obs0.1507 38076 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 50 509 3073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932658
X-RAY DIFFRACTIONf_angle_d1.05943612
X-RAY DIFFRACTIONf_chiral_restr0.0627389
X-RAY DIFFRACTIONf_plane_restr0.0065457
X-RAY DIFFRACTIONf_dihedral_angle_d12.661964
LS refinement shellResolution: 1.6→1.62 Å
RfactorNum. reflection% reflection
Rfree0.1964 86 -
Rwork0.1616 1640 -
obs--46.99 %
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)
10.304547422543-0.141453394180.03965288673220.519885624995-0.2815408211910.164683342804-0.0217576075403-0.195677605975-0.22434263930.04977736555830.2731375780160.427056454790.0284041322054-0.2032859905720.2139011480160.06330694943290.01175489464480.02711096616960.1205868879140.03088954102840.153851424749-18.4007775818-2.2842907726815.8769899109
2-0.142834575490.1482339149330.2897121756410.1487953570910.0840796070950.491910279383-0.0590883889919-0.06327861173970.02280495907150.009750287750710.02436894948960.107660602463-0.02164569198290.0462310804670.05526511818620.0915501780382-0.004746727021310.006811594792850.11760658662-0.02014414551640.0745253131635-0.58989699264311.929435054130.7932475807
30.4362375604170.02183567829-0.6379346175310.3703804501960.1281527258640.805687162744-0.0972683987941-0.241404718819-0.08944448468510.1298670659180.0535604733356-0.163705497468-0.06588070031610.6678174258640.007760879620780.112409787154-0.0745922113043-0.02757184811220.200852460492-0.03700079570270.106260286914.315093896916.626527628430.9515924017
40.3481728975490.0868976785339-0.4606250284560.9283523961820.3907276984431.321147704960.11099937368-0.1670395171930.03372710386990.034521642744-0.1115637517180.09620171507270.0904464871170.4696838129010.178639942010.07240834642360.00611287093152-0.008775332145120.108932918186-0.001384085598370.0522564320516.9947254290410.681982812226.4539709746
50.0889429530390.02924278654510.04002101206120.00447158381206-0.01753520748120.257193631288-0.0728136192314-0.04899435786210.0144577828439-0.07416086089530.07213278564590.13574593871-0.3466675765840.02949406443670.02859173850340.09850198528710.0089721351864-0.03029866622610.0546998205621-0.01297355773790.102559509687-7.3950670667114.212365079111.6766256446
60.418154579530.270160875477-0.2788489075380.2445109667170.05838328969340.37555562779-0.031664473918-0.0090084279265-0.0327655161015-0.00107143705892-0.0155787433104-0.04311124733530.0222707405955-0.0138723028823-0.0002676645778640.0512174686151-0.000486249439191-0.000557447050860.0319707115873-0.0006940162365240.0592556132488-4.775522545960.3211412735675.72114152952
70.155603277999-0.131737526026-0.06318185099620.355110309292-0.2583818156460.3340979790690.088822610647-0.119403863682-0.05549397246680.0962869584089-0.0666004063069-0.1035309443250.0320563798055-0.0461746412161-0.04315402194030.0489354120317-0.001087960888170.00279567310820.0621633440361-0.002057388594390.0760195744864-2.72968048796-8.069728070355.59939099589
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 22 )A2 - 221 - 21
22chain 'A' and (resid 23 through 79 )A23 - 7922 - 78
33chain 'A' and (resid 80 through 113 )A80 - 11379 - 112
44chain 'A' and (resid 114 through 175 )A114 - 175113 - 174
55chain 'A' and (resid 176 through 192 )A176 - 192175 - 191
66chain 'A' and (resid 193 through 274 )A193 - 274192 - 273
77chain 'A' and (resid 275 through 402 )A - C275 - 402274

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