PDB-8hyk: CD-NTase EfCdnE in complex with intermediate pppU[2'-5']p

ID or keywords:

Entry

Database: PDB / ID: 8hyk

Title

CD-NTase EfCdnE in complex with intermediate pppU[2'-5']p

Components

EfCdnE

Keywords

TRANSFERASE / CD-NTase / cGAS / cyclic dinucleotide

Function / homology

Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Alpha Beta / Chem-NE0

Function and homology information

Biological species

Enterococcus faecalis EnGen0062 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.021 Å

Authors

Ko, T.-P. / Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.

Funding support

Taiwan, 2items

Citation

Journal: 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

Deposition	Jan 6, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8hyk.cif.gz	86.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8hyk.ent.gz	59.4 KB	Display	PDB format
PDBx/mmJSON format	8hyk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8hyk_validation.pdf.gz	795.2 KB	Display	wwPDB validaton report
Full document	8hyk_full_validation.pdf.gz	794.7 KB	Display
Data in XML	8hyk_validation.xml.gz	15.1 KB	Display
Data in CIF	8hyk_validation.cif.gz	21.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hy/8hyk ftp://data.pdbj.org/pub/pdb/validation_reports/hy/8hyk	HTTPS FTP

-
Related structure data

Related structure data	7x4aC 7x4cC 7x4fC 7x4gC 7x4pC 7x4qC 7x4tC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: EfCdnE

hetero molecules

36.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	41.418, 56.940, 64.812
Angle α, β, γ (deg.)	90.000, 97.019, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	EfCdnE Mass: 35751.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis EnGen0062 (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical	ChemComp-NE0 / [[(2R,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate Mass: 564.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₆N₂O₁₈P₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.03 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: sodium tartrate, PEG 3350, MgCl2, UTP

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97626 Å / Relative weight: 1
Reflection	Resolution: 2.02→30 Å / Num. obs: 19291 / % possible obs: 97.8 % / Redundancy: 5.9 % / R_merge(I) obs: 0.067 / Net I/σ(I): 24.5
Reflection shell	Resolution: 2.02→2.09 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.162 / Num. unique obs: 1849 / % possible all: 94.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.021→28.486 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.936 / SU B: 3.748 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2102	971	5.038 %
R_work	0.1651	18303	-
all	0.167	-	-
obs	-	19274	97.59 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 26.469 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.013 Å²	-0 Å²	-0.03 Å²
2-	-	0.074 Å²	0 Å²
3-	-	-	-0.077 Å²

Refinement step

Cycle: LAST / Resolution: 2.021→28.486 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2513	0	34	187	2734

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	2608
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2297
X-RAY DIFFRACTION	r_angle_refined_deg	1.453	1.663	3549
X-RAY DIFFRACTION	r_angle_other_deg	1.363	1.582	5285
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.72	5	305
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.833	24.15	147
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.282	15	435
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.336	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	349
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2979
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	640
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	517
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	2067
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1330
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1144
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	149
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.162	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.107	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.267	0.2	95
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.167	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	2.383	2.678	1223
X-RAY DIFFRACTION	r_mcbond_other	2.383	2.677	1222
X-RAY DIFFRACTION	r_mcangle_it	3.441	4.003	1527
X-RAY DIFFRACTION	r_mcangle_other	3.44	4.004	1528
X-RAY DIFFRACTION	r_scbond_it	2.827	2.935	1385
X-RAY DIFFRACTION	r_scbond_other	2.831	2.934	1352
X-RAY DIFFRACTION	r_scangle_it	4.309	4.298	2022
X-RAY DIFFRACTION	r_scangle_other	4.324	4.293	1969
X-RAY DIFFRACTION	r_lrange_it	5.614	31.162	3081
X-RAY DIFFRACTION	r_lrange_other	5.578	30.926	3009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.021-2.074	0.239	70	0.163	1269	X-RAY DIFFRACTION	92.0275
2.074-2.13	0.296	79	0.175	1291	X-RAY DIFFRACTION	99.06
2.13-2.192	0.265	62	0.176	1327	X-RAY DIFFRACTION	98.7909
2.192-2.259	0.22	57	0.166	1232	X-RAY DIFFRACTION	98.9256
2.259-2.332	0.197	59	0.145	1227	X-RAY DIFFRACTION	98.9231
2.332-2.414	0.226	54	0.162	1183	X-RAY DIFFRACTION	99.0392
2.414-2.504	0.198	46	0.162	1127	X-RAY DIFFRACTION	98.7374
2.504-2.606	0.254	68	0.176	1106	X-RAY DIFFRACTION	98.9048
2.606-2.721	0.22	60	0.184	1032	X-RAY DIFFRACTION	98.645
2.721-2.852	0.218	45	0.166	1010	X-RAY DIFFRACTION	98.9681
2.852-3.005	0.245	50	0.172	956	X-RAY DIFFRACTION	99.0157
3.005-3.185	0.213	60	0.167	910	X-RAY DIFFRACTION	98.9796
3.185-3.402	0.202	45	0.171	835	X-RAY DIFFRACTION	98.324
3.402-3.671	0.206	44	0.169	795	X-RAY DIFFRACTION	98.7059
3.671-4.015	0.163	36	0.16	697	X-RAY DIFFRACTION	94.4588
4.015-4.479	0.144	36	0.143	649	X-RAY DIFFRACTION	96.3432
4.479-5.153	0.165	38	0.144	555	X-RAY DIFFRACTION	92.8012
5.153-6.265	0.258	19	0.191	484	X-RAY DIFFRACTION	93.8433
6.265-8.674	0.214	28	0.164	374	X-RAY DIFFRACTION	94.8113
8.674-28.486	0.218	15	0.164	244	X-RAY DIFFRACTION	97.3684

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi