PDB-7wz5: Larimichthys crocea IFNi

ID or keywords:

Entry

Database: PDB / ID: 7wz5

Title

Larimichthys crocea IFNi

Components

Interferon C

Keywords

CYTOKINE /

interferon /

antiviral

Function / homology

Interferon alpha/beta/delta / Interferon alpha/beta domain /

cytokine receptor binding / Four-helical cytokine-like, core / defense response to virus / extracellular region / Interferon C

Function and homology information

Biological species

Larimichthys crocea (large yellow croaker)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.39 Å

Authors

Chen, J.J.

Funding support

China, 1items

Citation

Journal: J Immunol. / Year: 2022
Title: Molecular and Structural Basis of Receptor Binding and Signaling of a Fish Type I IFN with Three Disulfide Bonds.
Authors: Chen, J. / Guan, Y. / Guan, H. / Mu, Y. / Ding, Y. / Zou, J. / Ouyang, S. / Chen, X.

History

Deposition	Feb 17, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 8, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wz5.cif.gz	77.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7wz5.ent.gz	59.3 KB	Display	PDB format
PDBx/mmJSON format	7wz5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wz/7wz5 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/7wz5	HTTPS FTP

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Related structure data

Related structure data	3piwS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#128 - Aug 2010 Interferons similarity (4) #52 - Apr 2004 Growth Hormone similarity (1) #149 - May 2012 Leptin similarity (1)

Deposited unit

A: Interferon C

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	36.310, 60.620, 81.220
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Interferon C

Mass: 17975.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Larimichthys crocea (large yellow croaker)
Gene: D5F01_LYC18041 / Production host:

Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A3G3BTG1

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.71 %
Crystal grow	Temperature: 289.15 K / Method: evaporation Details: Calcium chloride dihydrate, BIS-TRIS, Polyethylene glycol monomethyl ether 550

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979176 Å
Detector	Type: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979176 Å / Relative weight: 1
Reflection	Resolution: 1.39→34 Å / Num. obs: 36077 / % possible obs: 97.85 % / Redundancy: 5 % / B_iso Wilson estimate: 22.47 Å² / CC_1/2: 0.997 / Net I/σ(I): 30.97
Reflection shell	Resolution: 1.39→1.43 Å / Num. unique obs: 36077 / CC_1/2: 0.708

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Processing

Software

Name	Version	Classification
PHENIX	1.13	refinement
xia2	1	data scaling
PDB_EXTRACT	1	data extraction
xia2	1	data reduction
PARROT	1	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3PIW

3piw

Resolution: 1.39→33.15 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2128	1817	5.04 %	RANDOM
R_work	0.1986	-	-	-
obs	0.1993	36077	97.86 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.39→33.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1256	0	14	97	1367

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1303
X-RAY DIFFRACTION	f_angle_d	0.829	1774
X-RAY DIFFRACTION	f_dihedral_angle_d	4.839	176
X-RAY DIFFRACTION	f_chiral_restr	0.073	196
X-RAY DIFFRACTION	f_plane_restr	0.005	230

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 (%)
1.39-1.43	0.3511	144	0.3288	2463	X-RAY DIFFRACTION	94
1.43-1.47	0.3158	129	0.286	2557	X-RAY DIFFRACTION	96
1.47-1.52	0.2479	124	0.2383	2569	X-RAY DIFFRACTION	96
1.52-1.57	0.2321	144	0.2082	2569	X-RAY DIFFRACTION	98
1.57-1.63	0.2164	145	0.1996	2614	X-RAY DIFFRACTION	98
1.63-1.71	0.212	143	0.2111	2609	X-RAY DIFFRACTION	98
1.71-1.8	0.2371	116	0.2125	2628	X-RAY DIFFRACTION	98
1.8-1.91	0.2309	151	0.204	2661	X-RAY DIFFRACTION	98
1.91-2.06	0.2152	147	0.1945	2640	X-RAY DIFFRACTION	99
2.06-2.27	0.1912	139	0.1811	2690	X-RAY DIFFRACTION	99
2.27-2.59	0.2131	131	0.1884	2719	X-RAY DIFFRACTION	99
2.59-3.27	0.1968	158	0.1983	2723	X-RAY DIFFRACTION	100
3.27-33.15	0.2116	146	0.1949	2818	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	5.8264	1.1959	-3.4766	4.6907	-1.3518	6.7865	0.1324	0.1558	0.1455	-0.0319	-0.0363	-0.2295	-0.057	0.2829	-0.1485	0.1701	0.0253	-0.0195	0.1559	-0.0166	0.213	25.2466	19.0814	54.4647
2	0.8004	1.6924	0.3547	5.1991	-0.9942	3.1629	-0.0545	-0.1668	-0.0725	0.5271	0.0818	-0.133	0.2316	0.2368	-0.0404	0.2248	0.0258	0.0054	0.2212	0.0301	0.2451	15.6118	1.6895	63.1062
3	4.8053	-3.682	0.2628	4.4609	1.0852	1.0338	-1.0721	-0.9102	-1.4217	-0.1961	0.0603	-0.3086	1.4348	1.1983	0.6969	0.4659	0.1499	0.1953	0.3993	0.0921	0.4356	34.9864	3.4861	44.3524
4	3.4628	-1.2818	-3.6509	3.4676	0.2836	4.5295	-0.0315	0.5978	-0.3261	-0.2012	-0.0394	0.1769	0.1805	-0.293	0.052	0.2291	-0.0036	-0.0324	0.2241	0.0092	0.17	17.2224	10.7836	47.5671
5	3.6825	-0.2196	-1.437	1.7888	0.2593	4.9858	0.1619	-0.8035	0.2885	0.7739	-0.2889	0.9412	0.1139	-0.7431	0.0675	0.4203	-0.0171	0.1461	0.3457	-0.0177	0.3707	6.2632	13.9946	66.3608
6	2.3165	0.0105	-0.3918	3.2886	-0.0372	2.485	0.0519	0.1112	0.5913	0.0833	-0.0385	0.2688	-0.6875	-0.485	-0.077	0.2222	0.0362	-0.0209	0.2112	0.0119	0.2809	16.1263	21.7103	53.5163
7	4.4814	2.1975	-0.8603	3.8937	-3.3938	4.6904	-0.1387	0.859	-0.7065	-1.2602	-0.0275	0.2381	0.9682	0.0001	0.2741	0.4655	0.0567	-0.0409	0.4927	-0.077	0.4468	18.476	7.9392	40.5359
8	6.8911	-0.3459	-0.6703	4.7089	0.8196	6.1166	-0.0361	0.1698	-0.3269	0.2361	-0.0389	0.4507	0.1661	-0.7122	0.0816	0.1681	-0.0267	-0.0174	0.2005	0.0396	0.2422	6.5626	2.964	56.0893
9	6.2104	0.9418	-2.3579	2.8926	-1.0332	3.6682	-0.0837	-0.3979	-0.3618	0.1667	-0.1102	-0.0458	0.1074	0.2685	0.1834	0.1901	0.0156	-0.0028	0.1354	0.0217	0.1431	19.9568	8.0884	59.3228
10	5.0333	-1.4833	-0.4026	2.2022	-1.8348	7.494	-0.0604	-0.076	0.0684	-0.3954	-0.2703	-0.6415	-0.1911	0.349	0.3043	0.19	0.0058	-0.0145	0.236	0.0443	0.237	33.57	16.7429	49.1775

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 42 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 43 through 52 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 53 through 73 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 74 through 86 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 87 through 103 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 104 through 116 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 117 through 132 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 133 through 154 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 155 through 162 )

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