PDB-3zn6: VP16-VP17 complex, a complex of the two major capsid proteins of ...

ID or keywords:

Entry

Database: PDB / ID: 3zn6

Title

VP16-VP17 complex, a complex of the two major capsid proteins of bacteriophage P23-77

Components

VP16
VP17

Keywords

VIRAL PROTEIN

Function / homology

Function and homology information

identical protein binding
Similarity search - Function

Biological species

THERMUS PHAGE P23-77 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 Å

Authors

Rissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.

Citation

Journal: Structure / Year: 2013
Title: Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of an Ancient Branch from a Major Virus Lineage.
Authors: Rissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.

History

Deposition	Feb 13, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2013	Group: Database references
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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	3zn6.cif.gz	170.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3zn6.ent.gz	134.4 KB	Display	PDB format
PDBx/mmJSON format	3zn6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3zn6_validation.pdf.gz	442.3 KB	Display	wwPDB validaton report
Full document	3zn6_full_validation.pdf.gz	444.1 KB	Display
Data in XML	3zn6_validation.xml.gz	19.5 KB	Display
Data in CIF	3zn6_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zn/3zn6 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/3zn6	HTTPS FTP

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Related structure data

Related structure data	3zmnSC 3zmoSC 3zn4C 3zn5C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1jk9-d 3i4x-d 1kcx-d 2yg1-d 3e7s-d 6aby-d 6ust-2 5z74-d 3o9l-d 5kkr-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: VP17

B: VP16

hetero molecules

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

1

A: VP17

B: VP16

hetero molecules

A: VP17

B: VP16

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.780, 69.610, 81.620
Angle α, β, γ (deg.)	90.00, 104.99, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-1166- CL
2	1	B-1167- NA
3	1	B-2151- HOH

#1: Protein	VP17 Mass: 31875.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS PHAGE P23-77 (virus) / Plasmid: PIR1 (ORF17/PET22B) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: C8CHL5
#2: Protein	VP16 Mass: 19127.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SUBUNIT OF A STRAND-SWAPPED HOMODIMER / Source: (gene. exp.) THERMUS PHAGE P23-77 (virus) / Plasmid: PIR2 (ORF16/PET22B) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: C8CHL4
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.07 Å³/Da / Density % sol: 40.5 % / Description: NONE
Crystal grow	Method: vapor diffusion, sitting drop / pH: 7 Details: SITTING DROP VAPOUR DIFFUSION SYSTEM IN A 96-WELL PLATE, 100 NL OF PROTEIN MIXTURE CONSISTING OF VP16 AND VP17 (1.7 MG/ML AND 2 MG/ML, RESPECTIVELY, IN 20 MM TRIS-BUFFER PH 7.4) MIXED IN 1:1 ...Details: SITTING DROP VAPOUR DIFFUSION SYSTEM IN A 96-WELL PLATE, 100 NL OF PROTEIN MIXTURE CONSISTING OF VP16 AND VP17 (1.7 MG/ML AND 2 MG/ML, RESPECTIVELY, IN 20 MM TRIS-BUFFER PH 7.4) MIXED IN 1:1 MOLAR RATIO, WAS MIXED WITH 100 NL SOLUTION CONSISTING OF 1.1 M DIAMMONIUM TARTRATE PH 7. ONE WELL-DIFFRACTING CRYSTAL THAT WAS USED FOR DATA COLLECTION TOOK THREE MONTHS TO GROW.

Crystal

Density Matthews: 2.07 Å³/Da / Density % sol: 40.5 % / Description: NONE

Crystal grow

Method: vapor diffusion, sitting drop / pH: 7
Details: SITTING DROP VAPOUR DIFFUSION SYSTEM IN A 96-WELL PLATE, 100 NL OF PROTEIN MIXTURE CONSISTING OF VP16 AND VP17 (1.7 MG/ML AND 2 MG/ML, RESPECTIVELY, IN 20 MM TRIS-BUFFER PH 7.4) MIXED IN 1:1 ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.071
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.071 Å / Relative weight: 1
Reflection	Resolution: 1.53→39.6 Å / Num. obs: 61458 / % possible obs: 98.4 % / Redundancy: 6.3 % / B_iso Wilson estimate: 23.42 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 17.7
Reflection shell	Resolution: 1.53→1.57 Å / Redundancy: 4.4 % / R_merge(I) obs: 1.02 / Mean I/σ(I) obs: 2.9 / % possible all: 83.3

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Processing

Software

Name	Version	Classification
BUSTER	2.11.4	refinement
xia2		data reduction
XDS		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3ZMO AND 3ZMN

3zmo

3zmn

Resolution: 1.53→22.4 Å / Cor.coef. F_o:F_c: 0.9637 / Cor.coef. F_o:F_c free: 0.9604 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.072 / SU R_free Blow DPI: 0.072 / SU R_free Cruickshank DPI: 0.071
Details: RESIDUES 1-45, 198-202 AND 27 A, RESIDUES 1-20 AND 166-173 ARE DISORDERED IN CHAIN B.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1974	3110	5.06 %	RANDOM
R_work	0.1717	-	-	-
obs	0.173	61425	98.1 %	-

Displacement parameters

B_iso mean: 28.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.0078 Å²	0 Å²	-2.7567 Å²
2-	-	-1.256 Å²	0 Å²
3-	-	-	2.2638 Å²

Refine analyze

Luzzati coordinate error obs: 0.185 Å

Refinement step

Cycle: LAST / Resolution: 1.53→22.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2878	0	2	395	3275

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	3020	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.07	4130	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1003	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		70	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		446	HARMONIC	5
X-RAY DIFFRACTION	t_it		3020	HARMONIC	10
X-RAY DIFFRACTION	t_nbd		0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	4.1
X-RAY DIFFRACTION	t_other_torsion	14.6
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		388	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies		8	HARMONIC	1
X-RAY DIFFRACTION	t_utility_distance		2	HARMONIC	1
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		3747	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.53→1.57 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2269	182	4.88 %
R_work	0.2096	3544	-
all	0.2105	3726	-
obs	-	-	98.1 %

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	0.7823	0.3405	0.3363	1.6417	-1.4734	2.6708	0.0543	-0.1337	0.0831	0.0064	-0.0762	-0.0915	-0.1417	0.1728	0.0219	-0.0194	-0.0348	0.0148	0.0123	-0.0352	-0.0471	41.2895	28.6704	25.3318
2	1.8339	-1.7307	0.419	0.631	0.2177	0.1048	0.0136	0.0054	0.0881	0.0664	-0.0677	0.1993	-0.2853	0.0615	0.0542	0.0157	-0.0167	0.0539	-0.0404	-0.0774	0.0387	35.9147	39.3827	20.5344
3	0.8828	0.59	-0.3276	1.9483	-0.0426	1.0954	-0.0814	0.0381	-0.1572	-0.0424	0.0833	-0.2127	0.0918	0.027	-0.0019	-0.0402	-0.0149	0.0154	-0.0052	-0.0265	-0.0483	33.5529	7.6597	26.5086
4	0.3604	0.3432	-0.3418	0.1513	1.0751	-0.1937	-0.007	-0.0108	0.0147	0.0248	-0.0092	-0.0249	-0.0031	0.0241	0.0162	0.0847	-0.1355	0.0495	0.0251	-0.0532	-0.0841	45.5079	38.6662	30.6779
5	0.9196	-0.6038	-0.2179	0.3267	0.3894	0.7215	0.1004	0.0029	0.0832	0.0052	-0.0367	0.103	-0.2514	-0.1453	-0.0637	0.0136	0.0063	0.0282	0.0292	-0.0176	-0.0513	25.507	28.9908	29.8076
6	0.1994	-0.6429	0.4574	0.8534	-0.4862	0.6795	0.0144	0.0102	0.0406	0.0943	-0.0234	0.1157	-0.1714	0.0424	0.009	0.0446	-0.0581	0.0664	-0.0419	-0.0622	-0.003	38.5103	40.4006	25.7301
7	0.8782	0.2772	-0.5082	3.3479	-0.3677	1.241	0.0653	-0.197	-0.0493	0.1133	-0.0718	-0.0601	-0.135	0.1998	0.0065	-0.0408	-0.0347	0.0011	0.0352	-0.02	-0.0385	38.9399	20.8077	28.7158
8	0.0538	0.1326	-0.1008	0.6155	0.6049	0.0027	0.0033	0.0447	0.0084	-0.0084	-0.0057	-0.0004	0.0107	0.0436	0.0024	0.0361	0.0224	-0.0119	-0.056	-0.0216	0.0316	37.8546	41.4473	14.9596
9	0.2103	0.0675	-0.165	0	0.0849	-0.0978	-0.0026	-0.0072	0.0061	-0.014	-0.0023	-0.0054	0.0101	0.0184	0.0049	-0.1344	-0.0386	-0.0375	-0.0071	-0.0499	0.0877	59.2938	23.0454	4.0219
10	3.1801	1.0498	-2.1384	1.4844	0.3447	0.11	0.0049	-0.1231	-0.0694	-0.0539	-0.0516	-0.0647	0.0086	0.1194	0.0467	-0.0301	0.0051	0.0009	-0.0126	0.0096	-0.014	38.6415	20.7417	2.9013
11	0.7853	-0.3919	-0.3945	0.5496	-0.1441	0.753	0.0478	0.0791	0.036	0.0056	-0.0854	0.0677	-0.0682	-0.1088	0.0376	0.0139	0.0004	-0.018	-0.0136	-0.0062	-0.0228	22.9496	25.8007	3.0041
12	0.683	0.0679	-0.6928	0.0281	-0.2507	0.7153	0.0326	0.1828	0.0556	0.0685	-0.0581	0.0545	-0.0862	-0.0023	0.0255	0.0307	0.0214	0.0207	-0.0064	0.0255	-0.0201	34.2107	33.1668	-5.2411
13	2.8104	0.3615	-1.2337	2.3058	-0.5477	2.8701	0.0547	-0.0509	0.1999	0.1526	0.0513	0.2983	-0.1707	-0.2528	-0.106	-0.014	0.0194	0.0238	-0.0167	-0.002	-0.0052	17.3141	25.4058	13.3137
14	1.4841	-0.8037	-0.2722	1.5325	0.0293	-0.2522	0.0104	-0.0292	0.0205	-0.0005	0.0367	-0.0522	-0.0485	-0.0007	-0.0471	0.0362	-0.0108	-0.0084	-0.042	-0.0174	0.0054	28.9005	38.2088	6.3388
15	1.0943	-0.0002	-0.5291	0.2501	0.0296	0.1908	0.0075	0.0652	0.0789	0.0362	-0.0228	-0.0128	-0.0498	0.0293	0.0153	0.0455	0.0692	0.0044	-0.0233	0.0252	-0.0271	25.6382	41.433	-2.8116
16	0.861	0.4737	-1.1646	1.662	-0.2998	0.294	-0.0078	0.1	-0.0069	-0.1591	0.0088	0.052	0.1797	-0.0796	-0.001	0.0069	-0.0184	-0.0239	-0.0082	0.0157	-0.0215	24.4691	20.8302	1.7461

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|46 - A\|76 }
2	X-RAY DIFFRACTION	2	{ A\|77 - A\|93 }
3	X-RAY DIFFRACTION	3	{ A\|94 - A\|190 }
4	X-RAY DIFFRACTION	4	{ A\|191 - A\|205 }
5	X-RAY DIFFRACTION	5	{ A\|206 - A\|227 }
6	X-RAY DIFFRACTION	6	{ A\|228 - A\|241 }
7	X-RAY DIFFRACTION	7	{ A\|242 - A\|263 }
8	X-RAY DIFFRACTION	8	{ A\|264 - A\|271 }
9	X-RAY DIFFRACTION	9	{ B\|21 - B\|27 }
10	X-RAY DIFFRACTION	10	{ B\|28 - B\|40 }
11	X-RAY DIFFRACTION	11	{ B\|41 - B\|76 }
12	X-RAY DIFFRACTION	12	{ B\|77 - B\|91 }
13	X-RAY DIFFRACTION	13	{ B\|92 - B\|114 }
14	X-RAY DIFFRACTION	14	{ B\|115 - B\|125 }
15	X-RAY DIFFRACTION	15	{ B\|126 - B\|136 }
16	X-RAY DIFFRACTION	16	{ B\|137 - B\|165 }

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