PDB-9t3j: Protease from Norovirus Sydney GII.4 strain with crystallization ...

ID or keywords:

Entry

Database: PDB / ID: 9t3j

Title

Protease from Norovirus Sydney GII.4 strain with crystallization epitope mutation H50Y

Components

Genome polyprotein

Keywords

VIRAL PROTEIN / crystal epitopes / protease / Norovirus

Function / homology

Function and homology information

ribonucleoside triphosphate phosphatase activity / host cell / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function

Biological species

Norovirus Sydney 2212

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.411 Å

Authors

Fairhead, M. / MacLean, E.M. / Ni, X. / Wright, N.D. / Koekemoer, L. / von Delft, F.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / ...

History

Deposition	Oct 27, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9t3j.cif.gz	261.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9t3j.ent.gz	209 KB	Display	PDB format
PDBx/mmJSON format	9t3j.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/t3/9t3j ftp://data.pdbj.org/pub/pdb/validation_reports/t3/9t3j	HTTPS FTP

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Related structure data

Related structure data	8ru1C 8ru5C 9gdkC 9gh3C 9giiC 9gleC 9gp1C 9gp4C 9h44C 9t29C 9t2dC 9t2eC 9t2fC 9t2gC 9t2hC 9t31C 9t4pC C: citing same article (ref.)
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	#20 - Aug 2001 Poliovirus and Rhinovirus similarity (4)

Deposited unit

A: Genome polyprotein

B: Genome polyprotein

C: Genome polyprotein

D: Genome polyprotein

73.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Genome polyprotein

defined by author
Evidence: gel filtration
18.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Genome polyprotein

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

3

C: Genome polyprotein

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

4

D: Genome polyprotein

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

Unit cell

Length a, b, c (Å)	128.895, 128.895, 118.126
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	GLN	GLN	A	A	1 - 172	1 - 172
2	1	1	ALA	ALA	GLN	GLN	B	B	1 - 172	1 - 172
3	2	2	SER	SER	THR	THR	A	A	4 - 171	4 - 171
4	2	2	SER	SER	THR	THR	C	C	4 - 171	4 - 171
5	3	3	SER	SER	THR	THR	A	A	4 - 171	4 - 171
6	3	3	SER	SER	THR	THR	D	D	4 - 171	4 - 171
7	4	4	SER	SER	THR	THR	B	B	4 - 171	4 - 171
8	4	4	SER	SER	THR	THR	C	C	4 - 171	4 - 171
9	5	5	SER	SER	THR	THR	B	B	4 - 171	4 - 171
10	5	5	SER	SER	THR	THR	D	D	4 - 171	4 - 171
11	6	6	SER	SER	GLN	GLN	C	C	4 - 172	4 - 172
12	6	6	SER	SER	GLN	GLN	D	D	4 - 172	4 - 172

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Genome polyprotein Mass: 18437.412 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus Sydney 2212 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q8EAF6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 3.84 Å³/Da / Density % sol: 67.98 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ligand-friendly screen, condition F02 20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 6.5 0.2M sodium bromide

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976269 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976269 Å / Relative weight: 1
Reflection	Resolution: 2.41→81.132 Å / Num. obs: 43061 / % possible obs: 100 % / Redundancy: 42.5 % / CC_1/2: 0.999 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.41→2.45 Å / Num. unique obs: 2130 / CC_1/2: 0.413

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431 (refmacat 0.4.105)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.411→81.132 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.935 / SU B: 14.977 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.234
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.252	1740	4.395 %	RANDOM
R_work	0.2093	37846	-	-
all	0.211	-	-	-
obs	-	39586	92.026 %	-

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: 89.056 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.569 Å²	0.784 Å²	0 Å²
2-	-	1.569 Å²	-0 Å²
3-	-	-	-5.089 Å²

Refinement step

Cycle: LAST / Resolution: 2.411→81.132 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5126	0	0	27	5153

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	5270
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	5083
X-RAY DIFFRACTION	r_angle_refined_deg	2.463	1.797	7141
X-RAY DIFFRACTION	r_angle_other_deg	0.946	1.737	11712
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.038	5	682
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.336	5	37
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.204	10	872
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.53	10	186
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	792
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	6235
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1205
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	814
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	4734
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	2451
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	2965
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	101
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.192	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	119
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.148	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	12.699	8.666	2734
X-RAY DIFFRACTION	r_mcbond_other	12.686	8.667	2734
X-RAY DIFFRACTION	r_mcangle_it	17.047	15.575	3414
X-RAY DIFFRACTION	r_mcangle_other	17.045	15.577	3415
X-RAY DIFFRACTION	r_scbond_it	13.465	9.192	2536
X-RAY DIFFRACTION	r_scbond_other	13.464	9.193	2537
X-RAY DIFFRACTION	r_scangle_it	17.791	16.725	3727
X-RAY DIFFRACTION	r_scangle_other	17.788	16.726	3728
X-RAY DIFFRACTION	r_lrange_it	20.871	91.034	5372
X-RAY DIFFRACTION	r_lrange_other	20.871	91.039	5373
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.106	0.05	4974
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.144	0.05	4535
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.157	0.05	4473
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.159	0.05	4404
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.157	0.05	4427
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.148	0.05	4527

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10588	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10588	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.14408	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.14408	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.1574	0.05007
3	6	D	X-RAY DIFFRACTION	Local ncs	0.1574	0.05007
4	7	B	X-RAY DIFFRACTION	Local ncs	0.15898	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.15898	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.15666	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.15666	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.14838	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.14838	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.411-2.473	0.477	29	0.423	1059	0.424	3195	0.81	0.858	34.0532	0.42
2.473-2.541	0.375	77	0.419	1713	0.417	3079	0.778	0.733	58.1358	0.414
2.541-2.615	0.461	132	0.449	2825	0.449	2986	0.766	0.78	99.0288	0.446
2.615-2.695	0.373	134	0.397	2807	0.396	2942	0.884	0.887	99.966	0.395
2.695-2.783	0.366	113	0.365	2697	0.365	2810	0.892	0.899	100	0.356
2.783-2.881	0.381	120	0.343	2604	0.345	2724	0.892	0.913	100	0.333
2.881-2.989	0.349	126	0.295	2516	0.298	2642	0.929	0.94	100	0.276
2.989-3.111	0.307	105	0.262	2443	0.263	2548	0.935	0.956	100	0.236
3.111-3.249	0.29	118	0.22	2326	0.223	2444	0.947	0.97	100	0.192
3.249-3.408	0.278	77	0.201	2245	0.203	2322	0.948	0.975	100	0.177
3.408-3.592	0.256	115	0.204	2113	0.206	2228	0.962	0.977	100	0.183
3.592-3.809	0.269	74	0.21	2046	0.211	2120	0.96	0.976	100	0.191
3.809-4.071	0.252	91	0.203	1873	0.205	1964	0.956	0.979	100	0.186
4.071-4.397	0.192	80	0.171	1759	0.172	1839	0.977	0.986	100	0.155
4.397-4.815	0.182	88	0.128	1608	0.131	1696	0.982	0.991	100	0.114
4.815-5.381	0.184	79	0.134	1463	0.137	1542	0.982	0.989	100	0.118
5.381-6.209	0.224	58	0.169	1303	0.171	1361	0.98	0.988	100	0.148
6.209-7.593	0.22	55	0.183	1098	0.185	1153	0.972	0.983	100	0.165
7.593-10.692	0.239	43	0.159	859	0.163	902	0.965	0.985	100	0.149
10.692-81.132	0.307	26	0.29	489	0.291	515	0.94	0.942	100	0.279

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