PDB-8xy2: Crystal structure of MPXV P1 protein S87P mutant

Basic information

• Entry: Database: PDB / ID: 8xy2
• Title: Crystal structure of MPXV P1 protein S87P mutant
• 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
• Biological species: Monkeypox virus
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
• Authors: Ni, X.C. / Lei, J.

Funding support

China, 1items

Organization	Grant number	Country
Ministry of Science and Technology (MoST, China)	2021YFF0702004	China

• Citation: Journal: To Be Published; Title: Crystal structure of MPXV P1 protein S87P mutant; 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

Assembly

Deposited unit

B: Protein OPG035

C: Protein OPG035

A: Protein OPG035

D: Protein OPG035

Summary:

• 64.7 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	64,702	4
Polymers	64,702	4
Non-polymers	0	0
Water	7,062	392

1

B: Protein OPG035

A: Protein OPG035

Summary:

• defined by author&software
• Evidence: gel filtration, cross-linking
• 32.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	32,351	2
Polymers	32,351	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	2120 Å2
ΔGint	-2 kcal/mol
Surface area	11180 Å2
Method	PISA

2

C: Protein OPG035

D: Protein OPG035

Summary:

• defined by author&software
• 32.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	32,351	2
Polymers	32,351	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	2180 Å2
ΔGint	-0 kcal/mol
Surface area	11290 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	59.366, 155.500, 131.736
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C2221

Components

#1: Protein

B C A D
Protein OPG035 / Protein N1

Details:

Mass: 16175.423 Da / Num. of mol.: 4 / Mutation: S87P
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

Details:

Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: N

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.35 ų/Da / Density % sol: 47.7 %
• Crystal grow: Temperature: 291 K / Method: vapor diffusion, sitting drop; Details: 14.4% w/v PEG 8000, 80 mM Sodium cacodylate/ Hydrochloric acid pH 6.5, 160 mM Calcium acetate, 20% v/v Glycerol

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2023
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97861 Å / Relative weight: 1
• Reflection: Resolution: 2.24→43.91 Å / Num. obs: 29804 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC_1/2: 0.999 / Net I/σ(I): 11.1
• Reflection shell: Resolution: 2.24→2.31 Å / Num. unique obs: 2712 / CC_1/2: 0.949

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: 8XY1

8xy1

Resolution: 2.24→42.461 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.932 / SU B: 9.132 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.241
Details: Hydrogens have been added in their riding positions

	Rfactor	Num. reflection	% reflection
Rfree	0.2718	1502	5.044 %
Rwork	0.2186	28274	-
all	0.221	-	-
obs	-	29776	99.923 %

• 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: 40.64 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	3.581 Å2	0 Å2	-0 Å2
2-	-	-0.975 Å2	0 Å2
3-	-	-	-2.605 Å2

Refinement step

Cycle: LAST / Resolution: 2.24→42.461 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3875	0	0	392	4267

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	3949
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3757
X-RAY DIFFRACTION	r_angle_refined_deg	1.529	1.646	5332
X-RAY DIFFRACTION	r_angle_other_deg	1.369	1.593	8665
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.189	5	462
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.22	21.146	253
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.312	15	749
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.424	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	512
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4355
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	893
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	896
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	3688
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1975
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1831
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.191	0.2	252
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.159	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.087	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.242	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	3.847	4.058	1854
X-RAY DIFFRACTION	r_mcbond_other	3.845	4.057	1853
X-RAY DIFFRACTION	r_mcangle_it	5.421	6.073	2311
X-RAY DIFFRACTION	r_mcangle_other	5.42	6.074	2312
X-RAY DIFFRACTION	r_scbond_it	4.59	4.48	2095
X-RAY DIFFRACTION	r_scbond_other	4.589	4.482	2096
X-RAY DIFFRACTION	r_scangle_it	6.804	6.545	3020
X-RAY DIFFRACTION	r_scangle_other	6.803	6.547	3021
X-RAY DIFFRACTION	r_lrange_it	8.429	46.697	4688
X-RAY DIFFRACTION	r_lrange_other	8.402	46.48	4621
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.079	0.05	3816
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.102	0.05	3716
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.098	0.05	3818
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.087	0.05	3774
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.077	0.05	3821
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.078	0.05	3779

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.24-2.298	0.37	119	0.32	2060	X-RAY DIFFRACTION	99.8168
2.298-2.361	0.355	100	0.299	2031	X-RAY DIFFRACTION	99.9062
2.361-2.429	0.387	121	0.299	1903	X-RAY DIFFRACTION	99.9506
2.429-2.504	0.422	105	0.299	1905	X-RAY DIFFRACTION	100
2.504-2.586	0.321	91	0.28	1853	X-RAY DIFFRACTION	99.9486
2.586-2.677	0.322	98	0.259	1790	X-RAY DIFFRACTION	100
2.677-2.778	0.292	95	0.22	1723	X-RAY DIFFRACTION	100
2.778-2.891	0.287	89	0.217	1651	X-RAY DIFFRACTION	100
2.891-3.019	0.312	89	0.227	1581	X-RAY DIFFRACTION	100
3.019-3.167	0.263	77	0.23	1548	X-RAY DIFFRACTION	99.9385
3.167-3.338	0.291	81	0.233	1455	X-RAY DIFFRACTION	99.9349
3.338-3.54	0.244	71	0.213	1389	X-RAY DIFFRACTION	99.8632
3.54-3.783	0.227	60	0.19	1321	X-RAY DIFFRACTION	100
3.783-4.086	0.223	54	0.182	1221	X-RAY DIFFRACTION	100
4.086-4.474	0.221	50	0.168	1123	X-RAY DIFFRACTION	100
4.474-5	0.209	54	0.147	1038	X-RAY DIFFRACTION	99.9085
5-5.77	0.221	57	0.189	904	X-RAY DIFFRACTION	100
5.77-7.057	0.315	40	0.225	785	X-RAY DIFFRACTION	99.8789
7.057-9.94	0.161	35	0.176	621	X-RAY DIFFRACTION	99.8478
9.94-42.46	0.281	16	0.247	373	X-RAY DIFFRACTION	97.9849