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- PDB-7x4c: Native CD-NTase EfCdnE -

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Basic information

Entry
Database: PDB / ID: 7x4c
TitleNative CD-NTase EfCdnE
ComponentsEfCdnE
KeywordsTRANSFERASE / CD-NTase / cGAS / cyclic dinucleotide
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 2, 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

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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)35,9022
Polymers35,7511
Non-polymers1501
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint2 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.322, 57.104, 64.845
Angle α, β, γ (deg.)90.000, 97.101, 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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: sodium tartrate, PEG 3350

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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 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 29511 / % possible obs: 97.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.98 Å2 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.022 / Net I/σ(I): 35.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 15.1 / Num. unique obs: 2981 / CC1/2: 0.988 / Rpim(I) all: 0.049 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
CNSphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X4A

7x4a


Resolution: 1.75→26.98 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1985 1479 5.02 %
Rwork0.168 27966 -
obs0.1695 29445 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.08 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 10 418 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432595
X-RAY DIFFRACTIONf_angle_d0.65263522
X-RAY DIFFRACTIONf_chiral_restr0.0494381
X-RAY DIFFRACTIONf_plane_restr0.0036454
X-RAY DIFFRACTIONf_dihedral_angle_d17.4408935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.22941420.17932532X-RAY DIFFRACTION96.53
1.81-1.870.21280.16872533X-RAY DIFFRACTION97.58
1.87-1.940.21311210.16362536X-RAY DIFFRACTION97.54
1.94-2.030.23751160.17252565X-RAY DIFFRACTION97.17
2.03-2.140.21641370.17632543X-RAY DIFFRACTION97.21
2.14-2.270.25921320.19352547X-RAY DIFFRACTION96.78
2.27-2.450.24621370.21282500X-RAY DIFFRACTION96.38
2.45-2.70.24421370.20492527X-RAY DIFFRACTION96.35
2.7-3.090.18821330.17362547X-RAY DIFFRACTION96.96
3.09-3.890.17891590.13922559X-RAY DIFFRACTION97.52
3.89-26.980.14391370.14182577X-RAY DIFFRACTION95.8
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)
10.225016616855-0.03975197476620.06046360498970.393494227086-0.2495532754450.1507799120710.0266258636864-0.167838131369-0.1057042073050.007225979147910.163424507670.344723287863-0.0701762180196-0.06567729406210.2312472103690.08975877003430.02518751809040.02582347558410.1686532745310.003695481105570.172812951061-18.5071688488-8.2278883227316.078096066
2-0.001080943880080.1174452947630.2609523220880.105361248160.1398746379940.2010068311540.00834386679643-0.06793857702760.0176508021794-0.00670183360827-0.03326739463650.02627552514780.0240590360273-0.007232994423291.03935340083E-50.131862423738-0.02293295769330.003292714742430.137207113511-0.01905137494790.113146415161-0.3685932281435.9676745226530.9079215746
30.458699338004-0.061552640797-0.1319185113350.2275064985070.6889562803381.11467110349-0.0342662347745-0.0762816459968-0.00517255859887-0.008998061094960.0061909240524-0.005256948928510.02232680859530.189668488246-0.01386383378870.110052888732-0.0146618992065-0.003792548450090.115033677298-0.008815456046960.09782387243179.210493521847.5623538513529.1841001467
40.3611767279740.13842492210.1421416110620.1474794476810.1632625025760.353869312124-0.01445474282290.00502544627971-0.0290231818767-0.03241493083040.00618325547262-0.0352334522886-0.0154917311236-0.00370850007124-1.30234442451E-60.08786065065510.0017656140314-0.0005983039997660.08901641369460.001080298176430.0912679728929-3.11973786983-5.764750952917.40671818705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 307 )

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