PDB-6s1w: Crystal structure of dimeric M-PMV protease D26N mutant

ID or keywords:

Entry

Database: PDB / ID: 6s1w

Title

Crystal structure of dimeric M-PMV protease D26N mutant

Components

Gag-Pro-Pol polyprotein

Keywords

HYDROLASE /

Mason-Pfizer Monkey Virus / M-PMV /

retrovirus /

retropepsin /

aspartic protease /

dimerization / flap structure / apo

Function / homology

Function and homology information

dUTP diphosphatase /

dUTP diphosphatase activity /

Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases /

ribonuclease H / DNA integration /

RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency /

RNA-directed DNA polymerase activity /

Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...
Similarity search - Function

GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain /

dUTPase-like /

Biological species

Mason-Pfizer monkey virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.98 Å

Authors

Wosicki, S. / Gilski, M. / Jaskolski, M. / Zabranska, H. / Pichova, I.

Funding support

Czech Republic, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Comparison of a retroviral protease in monomeric and dimeric states.
Authors: Wosicki, S. / Gilski, M. / Zabranska, H. / Pichova, I. / Jaskolski, M.

History

Deposition	Jun 19, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6s1w.cif.gz	102.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6s1w.ent.gz	78.7 KB	Display	PDB format
PDBx/mmJSON format	6s1w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s1/6s1w ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s1w	HTTPS FTP

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Related structure data

Related structure data	6s1uSC 6s1vC 1az5 1bai 1ivp 2fmb 2rsp 3hvp 3liy 3slz 3sqf 4fiv 4hvp S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5c6c-d 4ej8-d 1hhp-1 5b18-1 3n6t-d 6f8h-2 5u0k-4 4z50-2 6dfy-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
Experimental dataset #1	Data reference: 10.18150/repod.7575322 / Data set type: diffraction image data / Metadata reference: 10.18150/repod.7575322

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (12) #163 - Jul 2013 HIV Capsid similarity (1) #135 - Mar 2011 Integrase similarity (1)

Deposited unit

B: Gag-Pro-Pol polyprotein

A: Gag-Pro-Pol polyprotein

25.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	49.987, 29.571, 85.200
Angle α, β, γ (deg.)	90.00, 102.52, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 1 - 108 / Label seq-ID: 1 - 108

Dom-ID	Auth asym-ID	Label asym-ID
1	B	A
2	A	B

#1: Protein	Gag-Pro-Pol polyprotein / Pr180 Mass: 12963.964 Da / Num. of mol.: 2 / Mutation: D26N; ENGINEERED MUTATION Source method: isolated from a genetically manipulated source Details: Gaps in the sequence indicate residues that were not modeled because of poor electron density. Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag-pro-pol / Plasmid: pBPS13ATG Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P07572, dUTP diphosphatase, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, ...References: UniProt: P07572, dUTP diphosphatase, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Gag-Pro-Pol polyprotein / Pr180

Mass: 12963.964 Da / Num. of mol.: 2 / Mutation: D26N; ENGINEERED MUTATION
Source method: isolated from a genetically manipulated source
Details: Gaps in the sequence indicate residues that were not modeled because of poor electron density.
Source: (gene. exp.)

Mason-Pfizer monkey virus / Gene: gag-pro-pol / Plasmid: pBPS13ATG
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07572, dUTP diphosphatase, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, ...

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.17 % / Description: plate
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Protein solution: 4.1 mg/mL protein, 5 mM TCEP, 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M sodium citrate buffer, 15% propan-2-ol, 5 mM TCEP;

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013
Radiation	Monochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.98→48.91 Å / Num. obs: 17123 / % possible obs: 98.9 % / Redundancy: 3.62 % / B_iso Wilson estimate: 25 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.119 / R_rim(I) all: 0.139 / Net I/σ(I): 8.24
Reflection shell	Resolution: 1.98→2.1 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.627 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2594 / CC_1/2: 0.521 / R_rim(I) all: 0.737 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
REFMAC	5.8.0232	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6S1U, chain A

6s1u

Resolution: 1.98→48.8 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.911 / SU B: 13.585 / SU ML: 0.169 / Cross valid method: FREE R-VALUE / ESU R: 0.183 / ESU R Free: 0.178 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26063	1000	5.8 %	RANDOM
R_work	0.19956	-	-	-
obs	0.20313	16122	98.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 34.024 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.18 Å²	0 Å²	0.22 Å²
2-	-	-2.45 Å²	-0 Å²
3-	-	-	-0.75 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→48.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1648	0	0	129	1777

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	1733
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	1625
X-RAY DIFFRACTION	r_angle_refined_deg	1.839	1.644	2370
X-RAY DIFFRACTION	r_angle_other_deg	1.385	1.58	3813
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.13	5	209
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.09	24.795	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.612	15	310
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.287	15	5
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	234
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1847
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	312
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.826	2.301	834
X-RAY DIFFRACTION	r_mcbond_other	1.809	2.298	833
X-RAY DIFFRACTION	r_mcangle_it	2.988	3.415	1039
X-RAY DIFFRACTION	r_mcangle_other	2.991	3.42	1040
X-RAY DIFFRACTION	r_scbond_it	1.977	2.51	899
X-RAY DIFFRACTION	r_scbond_other	1.976	2.514	900
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.085	3.696	1330
X-RAY DIFFRACTION	r_long_range_B_refined	6.31	26.745	1943
X-RAY DIFFRACTION	r_long_range_B_other	6.257	26.331	1923
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 2886 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	B
2	A

LS refinement shell

Resolution: 1.984→2.035 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.348	64	-
R_work	0.36	1033	-
obs	-	-	88.04 %

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	8.7409	4.0124	3.8193	5.6675	4.1914	3.2397	0.0949	-0.0292	-0.261	0.5366	0.048	-0.1438	0.3941	0.0719	-0.1429	0.1637	0.0804	-0.0318	0.1458	0.027	0.0659	22.8383	-5.5346	21.6498
2	1.3595	-0.3074	-2.1318	0.7839	0.288	6.4781	0.063	0.1607	-0.2023	0.0122	-0.2436	0.0603	0.1906	-0.3066	0.1805	0.177	0.0023	0.0192	0.1197	0.0001	0.0586	12.5942	-4.4991	33.4251
3	2.1945	1.4045	-1.0635	2.0299	-1.2242	4.8748	-0.0169	0.189	-0.1405	0.0367	-0.1239	0.098	0.0271	-0.2757	0.1408	0.1374	-0.0178	0.0125	0.1342	-0.0412	0.0598	7.4886	-1.1603	28.1903
4	0.211	-1.1556	0.4228	7.9406	-2.189	0.8759	-0.0587	-0.1012	-0.0127	0.2502	0.0397	0.2764	-0.0873	-0.2595	0.019	0.0986	0.0123	0.0316	0.2314	-0.0748	0.091	-2.023	1.9231	37.5496
5	7.9437	-2.3677	0.3284	1.7221	0.2186	0.9927	-0.1702	0.0778	-0.0299	0.2671	-0.0063	0.0873	0.013	0.0082	0.1766	0.1192	-0.0304	0.0413	0.0802	-0.0125	0.0484	10.169	3.7953	37.4268
6	1.2685	0.8345	-0.7064	0.7585	-0.0501	1.6117	0.0127	-0.0762	0.0982	0.0019	0.0436	0.0601	-0.045	0.0007	-0.0563	0.2321	0.0054	-0.0118	0.1628	-0.0088	0.0102	12.1777	2.9732	27.3093
7	11.4191	-2.7231	-2.0989	2.613	1.4209	3.3414	0.081	0.1012	-0.1183	-0.0141	0.0221	-0.0419	-0.1632	0.1139	-0.1031	0.1259	-0.0397	0.0002	0.0287	-0.0099	0.0329	21.5983	10.3697	20.6616
8	1.4918	0.4458	0.1115	2.4455	-0.2372	2.5295	0.051	0.0473	0.1309	0.0746	-0.0356	0.0672	-0.137	-0.1119	-0.0155	0.0121	0.01	0.0168	0.1673	0.0145	0.0791	13.5316	6.4008	4.4817
9	3.0247	3.9132	0.6571	5.3178	-0.401	7.1516	0.2385	-0.32	0.1396	0.2837	-0.3647	0.228	0.2029	-0.6861	0.1262	0.023	-0.0477	0.0092	0.27	-0.0874	0.1877	1.4819	-3.4553	7.2845
10	9.5497	3.9598	2.7234	3.2836	2.2688	1.5746	-0.0938	0.1442	-0.0253	-0.1114	0.1036	-0.0366	-0.0806	0.0501	-0.0097	0.0339	0.0068	0.0037	0.1264	0.0151	0.087	21.8727	1.3603	0.9387
11	1.714	-1.1977	0.7432	0.9326	-0.3246	2.5797	-0.0593	0.0087	-0.153	0.0909	0.0768	0.153	-0.0215	-0.0207	-0.0175	0.0695	-0.0048	0.0446	0.1751	0.0053	0.0919	13.382	1.7054	8.6623
12	3.568	-0.4799	4.6892	1.0797	-2.6918	10.4639	-0.1866	-0.0927	-0.1726	0.0198	-0.0965	-0.2333	-0.1341	0.2336	0.283	0.1429	0.099	0.0373	0.1812	-0.0031	0.1135	25.9622	0.7088	23.1317

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 19
3	X-RAY DIFFRACTION	3	A	20 - 38
4	X-RAY DIFFRACTION	4	A	39 - 58
5	X-RAY DIFFRACTION	5	A	59 - 79
6	X-RAY DIFFRACTION	6	A	80 - 108
7	X-RAY DIFFRACTION	7	B	1 - 9
8	X-RAY DIFFRACTION	8	B	10 - 45
9	X-RAY DIFFRACTION	9	B	46 - 63
10	X-RAY DIFFRACTION	10	B	64 - 79
11	X-RAY DIFFRACTION	11	B	80 - 102
12	X-RAY DIFFRACTION	12	B	103 - 108

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