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

ID or keywords:

Entry

Database: PDB / ID: 8jsj

Title

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Novosphingobium pentaromativorans

Components

PycTIR

Keywords

SIGNALING PROTEIN / cUMP receptor / Pycsar effector protein

Biological species

Novosphingobium pentaromativorans US6-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.858 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

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Download

PDBx/mmCIF format	8jsj.cif.gz	45.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8jsj.ent.gz	28.2 KB	Display	PDB format
PDBx/mmJSON format	8jsj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8jsj_validation.pdf.gz	425.9 KB	Display	wwPDB validaton report
Full document	8jsj_full_validation.pdf.gz	429.6 KB	Display
Data in XML	8jsj_validation.xml.gz	8.1 KB	Display
Data in CIF	8jsj_validation.cif.gz	10.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/js/8jsj ftp://data.pdbj.org/pub/pdb/validation_reports/js/8jsj	HTTPS FTP

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Related structure data

Related structure data	8jsfC 8jskC 8jszC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PycTIR

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	87.115, 87.115, 93.349
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	PycTIR Mass: 34018.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NCBI: WP_081473994.1 Source: (gene. exp.) Novosphingobium pentaromativorans US6-1 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate, 0.01 M calcium chloride dihydrate,0.05 M sodium cacodylate trihydrate pH 6.5,10% w/v polyethylene glycol 4,000

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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: 2.858→30 Å / Num. obs: 5229 / % possible obs: 99.8 % / Redundancy: 34.5 % / CC_1/2: 0.998 / Net I/σ(I): 85
Reflection shell	Resolution: 2.86→2.96 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 502 / CC_1/2: 0.895 / % possible all: 100

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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
Starting model: AlphaFold

Resolution: 2.858→24.345 Å / Cor.coef. F_o:F_c: 0.893 / Cor.coef. F_o:F_c free: 0.864 / SU B: 16.894 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 1.273 / ESU R Free: 0.401
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.282	247	5.04 %
R_work	0.2578	4654	-
all	0.259	-	-
obs	-	4901	93.817 %

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: 53.472 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.041 Å²	-0.021 Å²	-0 Å²
2-	-	-0.041 Å²	0 Å²
3-	-	-	0.134 Å²

Refinement step

Cycle: LAST / Resolution: 2.858→24.345 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1017	0	0	50	1067

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1024
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	1040
X-RAY DIFFRACTION	r_angle_refined_deg	1.451	1.633	1380
X-RAY DIFFRACTION	r_angle_other_deg	1.135	1.594	2383
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.969	5	132
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.882	21.818	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.793	15	191
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.384	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	138
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1151
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	217
X-RAY DIFFRACTION	r_nbd_refined	0.245	0.2	238
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.224	0.2	1028
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	471
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	542
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.204	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.065	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.282	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.246	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.208	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	4.218	5.291	534
X-RAY DIFFRACTION	r_mcbond_other	4.208	5.283	532
X-RAY DIFFRACTION	r_mcangle_it	6.882	7.907	664
X-RAY DIFFRACTION	r_mcangle_other	6.89	7.908	664
X-RAY DIFFRACTION	r_scbond_it	4.801	6.149	489
X-RAY DIFFRACTION	r_scbond_other	4.798	6.152	490
X-RAY DIFFRACTION	r_scangle_it	7.749	8.899	714
X-RAY DIFFRACTION	r_scangle_other	7.743	8.903	715
X-RAY DIFFRACTION	r_lrange_it	12.706	63.892	1103
X-RAY DIFFRACTION	r_lrange_other	12.761	63.957	1102

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 (%)
2.858-2.932	0.16	5	0.373	175	X-RAY DIFFRACTION	49.3151
2.932-3.011	0.313	15	0.414	241	X-RAY DIFFRACTION	70.137
3.011-3.097	0.472	13	0.411	317	X-RAY DIFFRACTION	96.2099
3.097-3.192	0.469	15	0.352	338	X-RAY DIFFRACTION	100
3.192-3.295	0.358	24	0.338	301	X-RAY DIFFRACTION	100
3.295-3.409	0.294	14	0.324	306	X-RAY DIFFRACTION	100
3.409-3.536	0.322	15	0.294	299	X-RAY DIFFRACTION	100
3.536-3.679	0.264	20	0.299	279	X-RAY DIFFRACTION	100
3.679-3.839	0.351	18	0.264	273	X-RAY DIFFRACTION	100
3.839-4.024	0.275	17	0.241	271	X-RAY DIFFRACTION	100
4.024-4.237	0.248	19	0.232	244	X-RAY DIFFRACTION	100
4.237-4.488	0.243	10	0.201	243	X-RAY DIFFRACTION	100
4.488-4.791	0.196	14	0.172	232	X-RAY DIFFRACTION	100
4.791-5.164	0.247	11	0.194	214	X-RAY DIFFRACTION	100
5.164-5.64	0.279	7	0.211	207	X-RAY DIFFRACTION	100
5.64-6.278	0.304	10	0.23	185	X-RAY DIFFRACTION	100
6.278-7.197	0.145	7	0.214	171	X-RAY DIFFRACTION	100
7.197-8.69	0.287	3	0.191	152	X-RAY DIFFRACTION	99.359
8.69-11.804	0.204	7	0.177	122	X-RAY DIFFRACTION	100
11.804-24.345	0.166	3	0.31	82	X-RAY DIFFRACTION	92.3913

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