PDB-8xy1: Crystal structure of MPXV P1 protein

ID or keywords:

Entry

Database: PDB / ID: 8xy1

Title

Crystal structure of MPXV P1 protein

Components

Protein OPG035

Keywords

VIRAL PROTEIN / MPXV / P1

Function / homology

Orthopoxvirus, Protein N1 / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / symbiont-mediated perturbation of host apoptosis / : / symbiont-mediated suppression of host NF-kappaB cascade / Protein OPG035

Function and homology information

Biological species

Monkeypox virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.575 Å

Authors

Ni, X.C. / Lei, J.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of MPXV P1 protein
Authors: Ni, X.C. / Lei, J.

History

Deposition	Jan 19, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xy1.cif.gz	160.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8xy1.ent.gz	124.1 KB	Display	PDB format
PDBx/mmJSON format	8xy1.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/xy/8xy1 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/8xy1	HTTPS FTP

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Related structure data

Related structure data	2i39S 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

Deposited unit

A: Protein OPG035

B: Protein OPG035

F: Protein OPG035

E: Protein OPG035

C: Protein OPG035

D: Protein OPG035

97 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein OPG035

B: Protein OPG035

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

2

F: Protein OPG035

E: Protein OPG035

defined by author&software
32.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Protein OPG035

D: Protein OPG035

defined by author&software
32.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	114.417, 114.417, 126.789
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

#1: Protein	Protein OPG035 / Protein N1 Mass: 16165.386 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: OPG035, P1L, MPXVgp023 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTN4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.47 Å³/Da / Density % sol: 50.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.8 M Succinic acid, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979152 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979152 Å / Relative weight: 1
Reflection	Resolution: 2.57→99.09 Å / Num. obs: 30914 / % possible obs: 100 % / Redundancy: 16 % / CC_1/2: 0.998 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.57→2.71 Å / Num. unique obs: 4468 / CC_1/2: 0.74

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2I39

2i39

Resolution: 2.575→99 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.93 / SU B: 11.247 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.286
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2418	1489	4.84 %
R_work	0.1961	29274	-
all	0.198	-	-
obs	-	30763	99.46 %

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: 50.587 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.752 Å²	0.376 Å²	0 Å²
2-	-	0.752 Å²	-0 Å²
3-	-	-	-2.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.575→99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5840	0	0	113	5953

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	5961
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	5659
X-RAY DIFFRACTION	r_angle_refined_deg	1.597	1.643	8042
X-RAY DIFFRACTION	r_angle_other_deg	1.371	1.594	13049
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.346	5	705
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.408	21.123	383
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.255	15	1136
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.195	15	67
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	772
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6605
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1360
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1184
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	5023
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	2963
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2809
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	115
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.233	0.2	29
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.045	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	4.712	4.902	2814
X-RAY DIFFRACTION	r_mcbond_other	4.709	4.901	2813
X-RAY DIFFRACTION	r_mcangle_it	6.775	7.352	3509
X-RAY DIFFRACTION	r_mcangle_other	6.775	7.354	3510
X-RAY DIFFRACTION	r_scbond_it	6.604	5.721	3147
X-RAY DIFFRACTION	r_scbond_other	6.603	5.723	3148
X-RAY DIFFRACTION	r_scangle_it	10.009	8.246	4529
X-RAY DIFFRACTION	r_scangle_other	10.008	8.248	4530
X-RAY DIFFRACTION	r_lrange_it	11.994	55.537	6701
X-RAY DIFFRACTION	r_lrange_other	11.998	55.544	6695
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.072	0.05	3753
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.059	0.05	3864
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.095	0.05	3754
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.064	0.05	3842
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.088	0.05	3735
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.083	0.05	3789
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.087	0.05	3796
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.081	0.05	3747
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.076	0.05	3852
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.088	0.05	3808
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.067	0.05	3850
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.085	0.05	3799
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.091	0.05	3769
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.081	0.05	3808
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.091	0.05	3735

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 (%)
2.575-2.642	0.323	89	0.275	2178	X-RAY DIFFRACTION	99.9559
2.642-2.714	0.36	117	0.266	2080	X-RAY DIFFRACTION	100
2.714-2.793	0.249	93	0.264	2045	X-RAY DIFFRACTION	100
2.793-2.879	0.299	101	0.253	1987	X-RAY DIFFRACTION	100
2.879-2.973	0.27	93	0.216	1894	X-RAY DIFFRACTION	100
2.973-3.077	0.279	107	0.219	1861	X-RAY DIFFRACTION	100
3.077-3.193	0.286	96	0.218	1789	X-RAY DIFFRACTION	100
3.193-3.324	0.297	85	0.204	1725	X-RAY DIFFRACTION	100
3.324-3.471	0.264	89	0.191	1668	X-RAY DIFFRACTION	100
3.471-3.641	0.241	77	0.209	1521	X-RAY DIFFRACTION	95.976
3.641-3.837	0.29	87	0.267	1431	X-RAY DIFFRACTION	94.9937
3.837-4.07	0.234	75	0.178	1442	X-RAY DIFFRACTION	99.9341
4.07-4.35	0.163	83	0.151	1332	X-RAY DIFFRACTION	99.9294
4.35-4.699	0.183	51	0.146	1282	X-RAY DIFFRACTION	100
4.699-5.146	0.197	57	0.154	1185	X-RAY DIFFRACTION	99.9195
5.146-5.753	0.288	52	0.159	1059	X-RAY DIFFRACTION	100
5.753-6.64	0.19	54	0.174	946	X-RAY DIFFRACTION	100
6.64-8.127	0.205	40	0.157	820	X-RAY DIFFRACTION	100
8.127-11.47	0.194	26	0.129	650	X-RAY DIFFRACTION	99.8523
11.47-99	0.142	17	0.26	379	X-RAY DIFFRACTION	96.3504

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