PDB-8jsk: Crystal structure of an N-terminal cyclic nucleotide-binding doma...

ID or keywords:

Entry

Database: PDB / ID: 8jsk

Title

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Pseudovibrio sp. in complex with cUMP

Components

PycTIR

Keywords

SIGNALING PROTEIN / cUMP receptor / Pycsar effector protein

Function / homology

Uridine-3',5'-cyclic monophosphate

Function and homology information

Biological species

Pseudovibrio sp. W64 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.401 Å

Authors

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

Funding support

Taiwan, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system.
Authors: Hou, M.H. / Chen, C.J. / Yang, C.S. / Wang, Y.C. / Chen, Y.

History

Deposition	Jun 20, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2024	Group: Database references / Structure summary / Category: citation / citation_author / entity 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 / _entity.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8jsk.cif.gz	79.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8jsk.ent.gz	57.1 KB	Display	PDB format
PDBx/mmJSON format	8jsk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8jsk_validation.pdf.gz	745.8 KB	Display	wwPDB validaton report
Full document	8jsk_full_validation.pdf.gz	749.1 KB	Display
Data in XML	8jsk_validation.xml.gz	14.5 KB	Display
Data in CIF	8jsk_validation.cif.gz	19.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/js/8jsk ftp://data.pdbj.org/pub/pdb/validation_reports/js/8jsk	HTTPS FTP

-
Related structure data

Related structure data	8jsfC 8jsjC 8jszC 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: PycTIR

B: PycTIR

hetero molecules

36 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PycTIR

hetero molecules

B: PycTIR

defined by author&software
Evidence: gel filtration
36 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	133.485, 133.485, 34.069
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

#1: Protein	PycTIR Mass: 17846.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NCBI: KZK76288.1; cloning site: L151, E152 Tag: H153-H158 Source: (gene. exp.) Pseudovibrio sp. W64 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-6SY / Uridine-3',5'-cyclic monophosphate / cUMP Mass: 306.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₁N₂O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.13 Å³/Da / Density % sol: 42.14 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.075 M HEPES pH 7.5, 7.5% w/v polyethylene glycol 8,000, 6% v/v ethylene glycol and 25% v/v glycerol

-
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 EIGER2 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: 2.401→30 Å / Num. obs: 12049 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC_1/2: 1 / Net I/σ(I): 23.6
Reflection shell	Resolution: 2.41→2.5 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1192 / CC_1/2: 0.808 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP	11.7.03	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.401→25.082 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.916 / SU B: 10.073 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.844 / ESU R Free: 0.288
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2436	664	5.555 %
R_work	0.1979	11289	-
all	0.2	-	-
obs	-	11953	98.826 %

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: 37.905 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.034 Å²	-0 Å²	-0 Å²
2-	-	0.034 Å²	-0 Å²
3-	-	-	-0.069 Å²

Refinement step

Cycle: LAST / Resolution: 2.401→25.082 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2498	0	20	88	2606

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	2552
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2489
X-RAY DIFFRACTION	r_angle_refined_deg	1.33	1.632	3438
X-RAY DIFFRACTION	r_angle_other_deg	1.149	1.581	5719
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.672	5	314
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.703	23.38	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.089	15	490
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.812	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	351
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2885
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	559
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	477
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	2322
X-RAY DIFFRACTION	r_nbtor_refined	0.145	0.2	1168
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1339
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	70
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	125
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.218	0.2	15
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.077	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.808	3.787	1263
X-RAY DIFFRACTION	r_mcbond_other	2.806	3.785	1262
X-RAY DIFFRACTION	r_mcangle_it	4.297	5.669	1574
X-RAY DIFFRACTION	r_mcangle_other	4.297	5.672	1575
X-RAY DIFFRACTION	r_scbond_it	3.194	4.265	1289
X-RAY DIFFRACTION	r_scbond_other	3.193	4.267	1290
X-RAY DIFFRACTION	r_scangle_it	5.203	6.213	1864
X-RAY DIFFRACTION	r_scangle_other	5.202	6.216	1865
X-RAY DIFFRACTION	r_lrange_it	7.324	44.051	2636
X-RAY DIFFRACTION	r_lrange_other	7.324	44.046	2635

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 (%)
2.401-2.463	0.278	31	0.237	776	X-RAY DIFFRACTION	92.0182
2.463-2.53	0.286	48	0.232	770	X-RAY DIFFRACTION	96.4623
2.53-2.603	0.278	56	0.221	770	X-RAY DIFFRACTION	99.2788
2.603-2.682	0.374	47	0.226	759	X-RAY DIFFRACTION	100
2.682-2.769	0.271	53	0.23	724	X-RAY DIFFRACTION	100
2.769-2.866	0.318	49	0.23	720	X-RAY DIFFRACTION	99.8701
2.866-2.973	0.293	39	0.233	685	X-RAY DIFFRACTION	100
2.973-3.093	0.285	40	0.221	691	X-RAY DIFFRACTION	99.8634
3.093-3.229	0.196	35	0.208	609	X-RAY DIFFRACTION	99.845
3.229-3.385	0.254	47	0.215	622	X-RAY DIFFRACTION	100
3.385-3.565	0.29	30	0.216	589	X-RAY DIFFRACTION	99.8387
3.565-3.778	0.198	25	0.189	575	X-RAY DIFFRACTION	99.8336
3.778-4.034	0.165	20	0.184	524	X-RAY DIFFRACTION	99.6337
4.034-4.351	0.301	22	0.16	500	X-RAY DIFFRACTION	99.0512
4.351-4.756	0.149	16	0.15	471	X-RAY DIFFRACTION	99.7951
4.756-5.301	0.208	20	0.17	413	X-RAY DIFFRACTION	99.3119
5.301-6.09	0.222	29	0.211	361	X-RAY DIFFRACTION	99.7442
6.09-7.383	0.209	20	0.199	321	X-RAY DIFFRACTION	100
7.383-10.138	0.188	22	0.124	248	X-RAY DIFFRACTION	99.631
10.138-25.082	0.188	15	0.232	160	X-RAY DIFFRACTION	95.6284

-
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