PDB-6cb6: CRYSTAL STRUCTURE OF VACCINIA VIRUS A6 N-TERMINUS (SPACE GROUP C2)

ID or keywords:

Entry

Database: PDB / ID: 6cb6

Title

CRYSTAL STRUCTURE OF VACCINIA VIRUS A6 N-TERMINUS (SPACE GROUP C2)

Components

Protein A6

Keywords

VIRAL PROTEIN / VACCINIA VIRUS / A6 / POXVIRUSES / VIRION CORE PROTEIN / VIRION MORPHOGENESIS

Function / homology

Poxvirus A6 / Poxvirus A6 protein / virion component / host cell cytoplasm / Virion morphogenesis protein OPG132

Function and homology information

Biological species

Vaccinia virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Han, Y. / Zhang, B. / Deng, J.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of a lipid-bound viral membrane assembly protein reveals a modality for enclosing the lipid bilayer.
Authors: Pathak, P.K. / Peng, S. / Meng, X. / Han, Y. / Zhang, B. / Zhang, F. / Xiang, Y. / Deng, J.

History

Deposition	Feb 2, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6cb6.cif.gz	65.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6cb6.ent.gz	48.6 KB	Display	PDB format
PDBx/mmJSON format	6cb6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6cb6_validation.pdf.gz	414.7 KB	Display	wwPDB validaton report
Full document	6cb6_full_validation.pdf.gz	415.7 KB	Display
Data in XML	6cb6_validation.xml.gz	8.5 KB	Display
Data in CIF	6cb6_validation.cif.gz	10.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cb/6cb6 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cb6	HTTPS FTP

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Related structure data

Related structure data	6br8C 6br9C 6cb7C 4x3w PDB Unreleased entry C: citing same article (ref.)
Similar structure data	3v1d-2 5m6f-d 2ewh-d 3r5l-d 2krc-d 6e25-d 3vww-2 3i86-1 1nu0-2 5d47-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

Deposited unit

A: Protein A6

14.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	103.658, 34.759, 38.716
Angle α, β, γ (deg.)	90.00, 96.28, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Protein A6 Mass: 14377.603 Da / Num. of mol.: 1 / Mutation: E47A, K48A, K49A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: A6L / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 GOLD / References: UniProt: P20985
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.46 Å³/Da / Density % sol: 50.02 %
Crystal grow	Temperature: 293 K / Method: evaporation / Details: 0.15M CESIUM CHLORIDE, 15% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.76→50 Å / Num. obs: 23750 / % possible obs: 83.2 % / Redundancy: 3.5 % / R_sym value: 0.094 / Net I/σ(I): 21.6
Reflection shell	Resolution: 1.76→1.83 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 5.2 / R_sym value: 0.215 / % possible all: 49.3

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Processing

Software

Name	Version	Classification
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
PHENIX	1.6_289	refinement

Refinement

Method to determine structure:

SAD / Resolution: 1.8→24.43 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 0.06 / Phase error: 23.07

	R_factor	Num. reflection	% reflection
R_free	0.231	2330	10.04 %
R_work	0.187	-	-
obs	0.192	23209	92.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / B_sol: 59.95 Å² / k_sol: 0.44 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-9.5671 Å²	0 Å²	-1.6447 Å²
2-	-	12.7095 Å²	0 Å²
3-	-	-	-3.1423 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→24.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	940	0	0	103	1043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	956
X-RAY DIFFRACTION	f_angle_d	0.907	1293
X-RAY DIFFRACTION	f_dihedral_angle_d	14.659	342
X-RAY DIFFRACTION	f_chiral_restr	0.06	156
X-RAY DIFFRACTION	f_plane_restr	0.004	158

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 (%)
1.7979-1.8621	0.3144	197	0.2393	1829	X-RAY DIFFRACTION	82
1.8621-1.9366	0.2532	238	0.2179	2128	X-RAY DIFFRACTION	92
1.9366-2.0247	0.2404	236	0.207	2109	X-RAY DIFFRACTION	96
2.0247-2.1314	0.2566	246	0.182	2156	X-RAY DIFFRACTION	97
2.1314-2.2649	0.2227	254	0.176	2213	X-RAY DIFFRACTION	98
2.2649-2.4396	0.2144	242	0.18	2189	X-RAY DIFFRACTION	97
2.4396-2.6848	0.2152	239	0.1826	2155	X-RAY DIFFRACTION	97
2.6848-3.0727	0.2463	243	0.1853	2180	X-RAY DIFFRACTION	97
3.0727-3.8688	0.2081	234	0.1765	2089	X-RAY DIFFRACTION	92
3.8688-24.433	0.2176	201	0.1873	1831	X-RAY DIFFRACTION	82

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	0.0943	-0.0982	0.0173	0.0687	-0.0374	0.0315	-0.3617	-0.7105	-1.1209	1.0348	0.4169	-0.0766	1.1644	-0.0465	0.001	0.4095	0.0373	0.0076	0.2988	0.0494	0.3181	36.4674	22.2785	10.0579
2	0.0915	0.0979	0.086	0.2179	0.0354	0.1182	-0.2172	-0.3263	0.1061	0.3241	0.0329	0.574	-0.0239	-0.8972	-0.0003	0.2173	-0.0753	0.0384	0.2254	-0.0195	0.2245	31.7119	27.3861	0.9945
3	0.0806	-0.0326	0.06	0.1188	0.0476	0.0507	0.1242	0.8473	1.0119	-0.1851	-0.2497	1.3201	-0.8994	-0.7334	-0.0023	0.265	-0.0024	-0.079	0.3996	0.0524	0.3332	30.1671	29.6484	-9.0963
4	0.1395	0.0338	0.0482	0.0567	0.0681	0.0922	0.3885	0.5182	-1.0636	-0.1728	-0.1018	0.4889	0.4709	0.0255	-0.0012	0.2972	-0.0213	0.0008	0.3339	-0.1436	0.408	34.6762	19.7709	-6.849
5	4.8682	-1.9942	2.761	1.5032	-0.681	1.8603	-0.261	-1.4246	-1.1737	1.5444	0.3431	0.5218	-0.081	-0.6364	0.0255	0.3467	0.0101	0.0421	0.2118	0.0285	0.3929	42.9671	18.4253	3.3704
6	1.7068	1.2303	0.8633	2.1166	3.1677	5.6363	0.1012	-1.1572	-1.7612	1.757	0.4118	-0.2078	1.4088	0.9303	0.1031	0.3429	0.0591	-0.0199	0.2638	0.0856	0.3556	48.0471	23.6278	5.2081
7	0.2964	0.1451	-0.2358	0.1562	-0.1775	0.1933	-0.0254	0.139	0.295	-0.0688	-0.0529	0.1022	-0.0202	0.141	0.0002	0.232	0.0245	-0.0004	0.2266	0.013	0.2251	51.5045	35.0278	5.4361
8	0.0629	0.0039	-0.0829	0.0623	-0.0315	0.0965	-0.759	-0.7016	0.8946	0.1949	-0.0289	-0.4463	-0.5407	-0.2659	-0.0001	0.3207	0.0837	-0.0694	0.2838	-0.1032	0.2604	46.1463	38.3176	15.0979
9	0.9438	0.124	0.2582	0.1038	-0.0406	0.1319	-0.45	-0.8855	2.1863	0.614	0.3137	0.3145	-1.7061	-0.3172	0.0004	0.3388	0.0575	-0.05	0.193	-0.0588	0.5149	41.4618	42.8874	8.328
10	0.0437	-0.03	-0.0672	0.2099	0.171	0.1185	-0.0662	-1.0395	0.2734	0.5756	-0.0018	0.3398	0.4387	-0.3731	-0.0008	0.238	0.0027	-0.0281	0.3217	-0.0179	0.3541	43.9491	38.0157	1.3957
11	0.065	0.0551	0.0277	0.0432	0.0085	0.0664	-0.4522	0.1689	-0.4038	0.5256	0.3667	-0.3632	0.8606	0.2683	-0.0006	0.2636	0.0153	0.0246	0.3089	0.0242	0.2251	42.8013	27.6155	-4.2008
12	0.068	0.0498	-0.0811	0.0668	-0.0514	0.0548	-0.1442	0.4677	-0.5237	-0.3904	-0.0292	0.105	-0.2404	0.0463	0.0008	0.2864	-0.018	0.0641	0.3471	-0.0515	0.2203	40.0432	24.2917	-7.7401
13	0.213	0.146	0.0656	0.0719	0.043	0.0222	-0.233	-0.1997	0.8583	-0.2473	0.562	-0.3801	-0.3051	0.2849	0.0006	0.1948	0.0128	-0.0031	0.1981	0.0061	0.2219	36.8213	36.4967	-2.0054
14	0.2059	-0.1606	-0.0389	0.109	0.102	0.1396	-0.4409	0.2307	0.1812	-0.5349	-0.1762	0.2161	-0.5504	-0.8373	-0.0009	0.1876	0.0797	-0.018	0.3092	0.0493	0.3178	28.6764	40.14	1.6847
15	0.1344	-0.075	-0.0425	0.0579	-0.0214	0.0838	-0.366	-0.4235	0.1798	0.8961	0.1879	0.1493	-0.0754	-0.3722	0.0001	0.256	0.0623	0.0178	0.2704	0.0155	0.2683	29.2246	37.9333	7.8378
16	0.0671	-0.085	0.0481	0.0505	-0.0344	0.011	0.2113	-0.1569	0.0194	0.2048	-0.1763	0.5453	0.121	-0.4039	0.0008	0.2333	0.0229	-0.0075	0.1656	-0.0127	0.2213	37.3724	34.1485	8.9089
17	1.0884	0.2208	-1.07	0.4871	-0.9329	2.0172	-0.5106	0.9074	-0.3492	-1.3655	0.1935	1.2455	0.7956	-1.7683	-0.0116	0.3137	0.0191	-0.0191	0.4454	-0.0011	0.2692	42.9305	28.9907	11.7794
18	1.4918	-1.9911	-0.1943	2.8633	0.0063	0.4009	-0.51	-1.6437	0.0447	0.4589	0.2058	-0.9161	0.5069	0.9289	0.0332	0.2868	0.1052	0.0273	0.4767	0.0768	0.1945	53.0953	24.0707	15.9481

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 3:9)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 10:18)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 19:24)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 25:30)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 31:35)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 36:40)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 41:51)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 52:57)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 58:63)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 64:69)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 70:74)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 75:82)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 83:89)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 90:94)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 95:99)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 100:105)
17	X-RAY DIFFRACTION	17	(CHAIN A AND RESID 106:111)
18	X-RAY DIFFRACTION	18	(CHAIN A AND RESID 112:120)

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