PDB-2iph: X-ray Structure at 1.75 A Resolution of a Norovirus Protease Link...

ID or keywords:

Entry

Database: PDB / ID: 2iph

Title

X-ray Structure at 1.75 A Resolution of a Norovirus Protease Linked to an Active Site Directed Peptide Inhibitor

Components

Thiol protease P3C

Keywords

HYDROLASE/HYDROLASE INHIBITOR / BETA BARREL / ALPHA HELIX / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...
Similarity search - Function

Biological species

Southampton virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.75 Å

Authors

Hussey, R.J.

Citation

Journal: Biochemistry / Year: 2011
Title: A Structural Study of Norovirus 3C Protease Specificity: Binding of a Designed Active Site-Directed Peptide Inhibitor.
Authors: Hussey, R.J. / Coates, L. / Gill, R.S. / Erskine, P.T. / Coker, S.F. / Mitchell, E. / Cooper, J.B. / Wood, S. / Broadbridge, R. / Clarke, I.N. / Lambden, P.R. / Shoolingin-Jordan, P.M.

History

Deposition	Oct 12, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 23, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jun 20, 2012	Group: Database references
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2iph.cif.gz	92.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2iph.ent.gz	67.4 KB	Display	PDB format
PDBx/mmJSON format	2iph.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2iph_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	2iph_full_validation.pdf.gz	1.2 MB	Display
Data in XML	2iph_validation.xml.gz	21.3 KB	Display
Data in CIF	2iph_validation.cif.gz	28.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ip/2iph ftp://data.pdbj.org/pub/pdb/validation_reports/ip/2iph	HTTPS FTP

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Related structure data

Similar structure data	6yev-1 6zxv-1 6yev-3 5e71-d 2ht6-d 4euv-d 2hjm-d 5oi9-2 6zxy-d 4c05-d Search similar-shape structures by Omokage search (details) 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: Thiol protease P3C

B: Thiol protease P3C

hetero molecules

40.1 kDa, 2 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)	49.497, 84.106, 121.471
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Thiol protease P3C / 3C-like protease / 3C-pro Mass: 19305.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Southampton virus (serotype 3) / Genus: Norovirus / Species: Norwalk virus / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q04544, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical	ChemComp-LGG / N-ACETYL-L-ALPHA-GLUTAMYL-L-PHENYLALANYL-L-GLUTAMINYL-N-[(1S)-4-AMINO-1-(2-CARBOXYETHYL)-4-OXOBUTYL]-L-LEUCINAMIDE Mass: 733.809 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₅₁N₇O₁₁
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.67 %

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Data collection

Diffraction

ID	Crystal-ID
1	1
2	1
3	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)	Wavelength
SYNCHROTRON	ESRF	ID23-1	1	0.97625,0.97925,0.97955
SYNCHROTRON	ESRF	ID23-1	2		0.934

Detector

Type: MARRESEARCH / Detector: CCD / Date: Apr 5, 2004

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97625	1
2	0.97925	1
3	0.97955	1
4	0.934	1

Reflection

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	R_sym value	D res high (Å)	D res low (Å)	Num. obs	% possible obs
19.6	1	6.5	521622	0.086	0.086	2.2	40.456	26649	99.5
6.7	2	8.6	120862	0.057	0.057	2.5	46.045	18029	98.2
6.6	3	7.4	117483	0.064	0.064	2.5	49.147	17803	97.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
9.84	40.46	97.2	1	0.036	0.036	16.7
6.96	9.84	99.5	1	0.041	0.041	19.7
5.68	6.96	99.8	1	0.059	0.059	19.9
4.92	5.68	99.6	1	0.053	0.053	20.6
4.4	4.92	99.8	1	0.056	0.056	20.8
4.02	4.4	99.8	1	0.061	0.061	20.8
3.72	4.02	99.6	1	0.06	0.06	21.2
3.48	3.72	99.7	1	0.064	0.064	21.1
3.28	3.48	99.7	1	0.073	0.073	20.8
3.11	3.28	100	1	0.083	0.083	20.4
2.97	3.11	99.7	1	0.108	0.108	20
2.84	2.97	99.6	1	0.127	0.127	19.8
2.73	2.84	99.4	1	0.167	0.167	19.7
2.63	2.73	99.9	1	0.208	0.208	19.5
2.54	2.63	99.3	1	0.277	0.277	19.2
2.46	2.54	99.2	1	0.337	0.337	19.2
2.39	2.46	99.9	1	0.4	0.4	18.7
2.32	2.39	98.8	1	0.494	0.494	18.5
2.26	2.32	99.6	1	0.601	0.601	18.4
2.2	2.26	98.7	1	0.741	0.741	18
11.18	46.04	46.9	2	0.034	0.034	4.1
7.91	11.18	68.2	2	0.032	0.032	5.5
6.45	7.91	96.5	2	0.041	0.041	6.5
5.59	6.45	99.4	2	0.052	0.052	6.8
5	5.59	99.4	2	0.043	0.043	6.9
4.56	5	99.4	2	0.048	0.048	7
4.23	4.56	99.4	2	0.055	0.055	6.9
3.95	4.23	99.7	2	0.056	0.056	7
3.73	3.95	99.6	2	0.053	0.053	7.1
3.54	3.73	99.6	2	0.056	0.056	7.1
3.37	3.54	99.8	2	0.059	0.059	6.9
3.23	3.37	99.4	2	0.068	0.068	6.9
3.1	3.23	99.6	2	0.066	0.066	6.9
2.99	3.1	99.6	2	0.073	0.073	6.7
2.89	2.99	99.1	2	0.079	0.079	6.7
2.8	2.89	99.8	2	0.083	0.083	6.6
2.71	2.8	99.2	2	0.091	0.091	6.5
2.64	2.71	99.7	2	0.108	0.108	6.5
2.56	2.64	99	2	0.117	0.117	6.5
2.5	2.56	99.9	2	0.137	0.137	6.4
11.18	49.16	36.5	3	0.043	0.043	3.8
7.91	11.18	55.2	3	0.042	0.042	5.2
6.45	7.91	92.6	3	0.045	0.045	6.4
5.59	6.45	98.6	3	0.054	0.054	6.6
5	5.59	98.4	3	0.045	0.045	6.9
4.56	5	99	3	0.052	0.052	6.8
4.23	4.56	99	3	0.061	0.061	6.8
3.95	4.23	99.5	3	0.067	0.067	6.9
3.73	3.95	99.2	3	0.062	0.062	7
3.54	3.73	99.5	3	0.063	0.063	7
3.37	3.54	99.7	3	0.066	0.066	6.8
3.23	3.37	99.4	3	0.074	0.074	6.7
3.1	3.23	99.9	3	0.072	0.072	6.7
2.99	3.1	99.6	3	0.083	0.083	6.5
2.89	2.99	99.4	3	0.091	0.091	6.6
2.8	2.89	99.9	3	0.096	0.096	6.5
2.71	2.8	98.9	3	0.105	0.105	6.4
2.64	2.71	99.7	3	0.124	0.124	6.5
2.56	2.64	98.9	3	0.13	0.13	6.4
2.5	2.56	100	3	0.158	0.158	6.3

Reflection

Resolution: 1.7→36.491 Å / Num. obs: 55934 / % possible obs: 98.8 % / Redundancy: 6.7 % / R_merge(I) obs: 0.053 / R_sym value: 0.053 / Net I/σ(I): 8.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.7-1.79	5.2	0.623	1.2	38859	7504	0.623	92.8
1.79-1.9	6.7	0.385	2	51966	7740	0.385	99.9
1.9-2.03	6.9	0.206	3.6	50152	7259	0.206	100
2.03-2.19	7.1	0.127	5.8	47821	6782	0.127	100
2.19-2.4	7.2	0.09	7.9	45143	6291	0.09	100
2.4-2.69	7.2	0.06	11.8	41055	5687	0.06	100
2.69-3.1	7.2	0.041	15.8	36356	5067	0.041	100
3.1-3.8	7.1	0.031	18	30725	4326	0.031	100
3.8-5.38	6.8	0.034	16.2	22949	3366	0.034	99.6
5.38-40.49	5.9	0.032	19	11332	1912	0.032	97.3

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9793	4.7	-4.9
1	3 wavelength	2	0.9763	4	-4
1	3 wavelength	3	0.9795	2.3	-8.9

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	43.649	0.392	0.806	0.134	1.06
2	Se	46.504	0.435	0.731	0.016	1.131
3	Se	60	0.893	0.717	0.24	1.216
4	Se	60	0.363	0.934	0.147	0.865
5	Se	37.002	0.678	0.779	0.232	0.492
6	Se	48.936	0.402	0.153	0.232	0.789
7	Se	47.164	0.573	0.606	0.095	0.472
8	Se	60	0.428	0.028	0.215	1.09
9	Se	60	0.588	0.135	0.235	0.685
10	Se	60	0.438	0.805	0.222	0.573

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Processing

Software

Name	Version	Classification
SCALA		data scaling
SOLVE	2.08	phasing
RESOLVE		phasing
CNS		refinement
PDB_EXTRACT	2	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.75→29.4 Å / FOM work R set: 0.869 / σ(F): 0

	R_factor	Num. reflection	% reflection
R_free	0.221	2580	5 %
R_work	0.204	-	-
obs	-	51760	99.6 %

Solvent computation

B_sol: 46.772 Å²

Displacement parameters

B_iso mean: 27.208 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.281 Å²	0 Å²	0 Å²
2-	-	-4.348 Å²	0 Å²
3-	-	-	4.629 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→29.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2667	0	104	247	3018

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	c_mcbond_it	1.364	1.5
X-RAY DIFFRACTION	c_scbond_it	1.936	2
X-RAY DIFFRACTION	c_mcangle_it	2.257	2
X-RAY DIFFRACTION	c_scangle_it	2.934	2.5

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs
1.75-1.76	0.324	49	0.296	937	986
1.76-1.77	0.302	47	0.318	954	1001
1.77-1.79	0.37	61	0.31	907	968
1.79-1.8	0.275	52	0.284	962	1014
1.8-1.81	0.329	55	0.294	992	1047
1.81-1.83	0.274	43	0.266	982	1025
1.83-1.84	0.347	53	0.255	969	1022
1.84-1.85	0.247	45	0.259	983	1028
1.85-1.87	0.322	56	0.261	963	1019
1.87-1.89	0.228	47	0.225	967	1014
1.89-1.9	0.227	48	0.214	995	1043
1.9-1.92	0.257	39	0.209	984	1023
1.92-1.93	0.297	32	0.206	984	1016
1.93-1.95	0.225	43	0.207	982	1025
1.95-1.97	0.319	45	0.203	986	1031
1.97-1.99	0.191	51	0.199	983	1034
1.99-2.01	0.227	78	0.2	922	1000
2.01-2.03	0.219	57	0.201	992	1049
2.03-2.05	0.231	48	0.206	989	1037
2.05-2.07	0.239	44	0.206	985	1029
2.07-2.1	0.268	47	0.204	948	995
2.1-2.12	0.227	55	0.194	990	1045
2.12-2.15	0.277	44	0.204	990	1034
2.15-2.18	0.235	47	0.214	978	1025
2.18-2.2	0.227	35	0.192	1000	1035
2.2-2.24	0.214	63	0.211	970	1033
2.24-2.27	0.215	52	0.204	981	1033
2.27-2.3	0.244	47	0.205	971	1018
2.3-2.34	0.285	63	0.208	1006	1069
2.34-2.38	0.241	76	0.218	938	1014
2.38-2.42	0.24	47	0.213	974	1021
2.42-2.46	0.223	63	0.198	983	1046
2.46-2.51	0.204	54	0.194	985	1039
2.51-2.56	0.251	55	0.207	978	1033
2.56-2.61	0.206	65	0.204	977	1042
2.61-2.67	0.192	50	0.201	976	1026
2.67-2.74	0.212	59	0.203	1001	1060
2.74-2.82	0.192	55	0.197	962	1017
2.82-2.9	0.205	54	0.195	1023	1077
2.9-2.99	0.214	47	0.211	978	1025
2.99-3.1	0.222	58	0.203	1006	1064
3.1-3.22	0.204	40	0.197	1001	1041
3.22-3.37	0.194	45	0.195	1019	1064
3.37-3.55	0.233	46	0.199	1001	1047
3.55-3.77	0.205	36	0.184	1013	1049
3.77-4.06	0.18	59	0.188	1015	1074
4.06-4.47	0.188	59	0.162	1002	1061
4.47-5.12	0.164	56	0.169	1011	1067
5.12-6.45	0.213	48	0.224	1048	1096
6.45-100	0.282	62	0.249	1037	1099

Xplor file

Refine-ID	Serial no	Param file
X-RAY DIFFRACTION	1	protein_rep.param
X-RAY DIFFRACTION	2	peptide2.param
X-RAY DIFFRACTION	3	water_rep.param

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