PDB-3kea: Structure function studies of vaccinia virus host-range protein K...

ID or keywords:

Entry

Database: PDB / ID: 3kea

Title

Structure function studies of vaccinia virus host-range protein K1 reveal a novel ankyrin repeat interaction surface for K1s function

Components

K1L

Keywords

VIRAL PROTEIN / K1L /

Vaccinia Virus /

tropism / ANK repeat

Function / homology

Function and homology information

Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats /

Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat /

Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology

Biological species

Vaccinia virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Li, Y.

Citation

Journal: J.Virol. / Year: 2010
Title: Structure function studies of vaccinia virus host range protein k1 reveal a novel functional surface for ankyrin repeat proteins.
Authors: Li, Y. / Meng, X. / Xiang, Y. / Deng, J.

History

Deposition	Oct 25, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 31, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kea.cif.gz	125.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3kea.ent.gz	107.9 KB	Display	PDB format
PDBx/mmJSON format	3kea.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/ke/3kea ftp://data.pdbj.org/pub/pdb/validation_reports/ke/3kea	HTTPS FTP

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Related structure data

Similar structure data	6xf1-2 4zlc-d 3o01-d 5mk2-d 3zkx-d 5mjz-d 5mjy-2 2ral-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: K1L

B: K1L

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

1

Idetical with deposited unit
defined by author

2

A: K1L

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

3

B: K1L

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

Unit cell

Length a, b, c (Å)	95.107, 110.263, 86.259
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	1 - 270
2	1	1	3	B	1 - 270

#1: Protein	K1L Mass: 33035.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Gene: K1L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IV60
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.42 Å³/Da / Density % sol: 64.06 %
Crystal grow	Temperature: 293 K / pH: 5 Details: 0.2M Natartrate, 20% PEG3350, 0.1M NaAc, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 77 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9793453, 0.9794771

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2007

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9793453	1
2	0.9794771	1

Reflection

Resolution: 2.3→39.28 Å / Num. obs: 37088

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
SHELXS		phasing
REFMAC	5.2.0019	refinement
HKL-3000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.3→39.28 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.93 / SU B: 14.239 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.254	1884	5.1 %	RANDOM
R_work	0.21	-	-	-
obs	0.212	35204	90.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 31.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	0 Å²
2-	-	0.23 Å²	0 Å²
3-	-	-	-0.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→39.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4536	0	0	226	4762

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	4436
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.436	1.956	5980
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.423	5	564
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.399	25.667	180
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.389	15	758
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.107	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	706
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3252
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	2054
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	3129
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	197
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	0.146	0.2	45
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.207	0.2	7
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	0.663	1.5	2867
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.138	2	4495
X-RAY DIFFRACTION	r_scbond_it	2.115	3	1778
X-RAY DIFFRACTION	r_scangle_it	2.946	4.5	1485
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
1076	tight positional	0.05	0.05
1006	loose positional	0.44	5
1076	tight thermal	0.16	0.5
1006	loose thermal	1.78	10

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	112	-
R_work	0.267	1948	-
obs	-	-	69.64 %

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	3.0778	-0.9006	-1.8837	30.5353	-8.976	10.4416	-0.1646	0.2482	-0.5276	-1.0011	0.1367	-1.6082	0.0142	0.8077	0.0279	-0.048	0.0096	0.0899	0.2414	-0.0026	0.2376	61.5895	10.4437	29.4135
2	1.9792	0.7848	-0.3641	3.832	-0.3667	1.0968	-0.032	0.3274	-0.1317	-0.3322	-0.0016	-0.0887	0.0835	0.2679	0.0336	0.0184	0.0106	0.0374	0.1308	-0.011	0.0379	52.6068	11.4665	26.1945
3	4.7932	0.9841	-1.2112	2.1825	-0.5311	4.3845	-0.1545	0.0963	0.2145	-0.181	-0.0305	0.0227	-0.1745	-0.2575	0.185	0.0382	0.0002	0.0125	0.0866	-0.0183	0.0616	42.1357	18.855	32.7407
4	4.8474	1.5677	0.392	3.7914	2.6863	8.1638	-0.0359	0.2299	-0.0899	0.0817	-0.0361	0.0471	0.2342	-0.0829	0.072	0.0169	-0.0197	0.0373	0.0377	-0.0139	0.059	36.1705	13.311	40.228
5	11.8509	-0.8874	0.2533	4.2444	-2.1586	1.1012	0.2243	0.7062	0.5463	-0.1949	-0.0908	0.0392	-0.031	0.3674	-0.1335	0.0253	0.0199	0.0264	0.1479	-0.0137	0.0268	32.9203	24.8832	38.3282
6	8.743	-3.9127	-0.5733	17.4303	1.6288	16.5725	-0.2209	0.0053	-0.394	0.3627	0.2551	1.013	0.5068	-0.8273	-0.0342	-0.0063	-0.0805	0.0052	0.2356	-0.0902	0.0702	25.8454	13.4516	40.156
7	9.7303	1.2598	2.6178	0.9995	3.1754	10.3243	-0.1127	0.0525	-0.0865	0.0409	0.0059	0.0402	0.0884	0.0338	0.1068	-0.0371	-0.0401	0.046	0.1131	-0.0177	0.0457	28.4559	20.2204	47.9486
8	1.4802	-0.8778	0.4192	10.3258	-12.2579	22.5716	-0.0814	0.9217	0.055	-0.5452	0.3485	0.6696	0.7586	-1.2459	-0.2671	-0.0183	-0.0642	0.007	0.1532	-0.0155	0.0746	20.6774	14.5751	51.8051
9	9.0269	-7.4552	5.2573	6.1572	-4.3419	3.0619	0.168	0.3636	-0.6605	0.2198	0.0604	0.6338	0.555	-0.3746	-0.2284	0.277	0.0003	0.0547	0.1682	-0.0468	0.2602	23.0371	20.669	57.7358
10	4.8101	-4.2905	3.8392	3.8272	-3.4487	7.2062	0.3665	0.0142	-0.7495	-0.6126	-0.0333	0.4667	1.0109	-0.1095	-0.3332	0.1362	0.0345	-0.0351	0.0282	-0.0098	0.0702	10.6228	19.8141	55.3991
11	15.1182	12.7672	2.4522	17.0643	9.3338	8.7941	0.5352	-0.4861	0.278	-0.2674	-0.2491	0.346	1.2976	0.6001	-0.2861	0.4274	-0.0458	0.2046	-0.1463	0.0202	0.0826	19.152	9.4185	67.2366
12	2.669	-1.0479	2.6395	2.7097	-1.5643	4.9914	0.2833	0.2635	-0.652	-0.1676	0.1152	0.0663	0.5825	-0.2537	-0.3985	0.0717	-0.0587	-0.0289	0.0242	0.0047	0.0805	14.398	15.5986	69.6586
13	1.1445	-2.6454	1.2372	7.3533	-6.0798	9.9284	0.0711	-0.3346	0.0867	0.0386	0.1049	-0.0563	0.1121	-0.2563	-0.1761	0.0319	-0.0038	0.0119	0.0604	-0.0085	0.0678	6.1084	23.3029	69.2851
14	9.1501	-0.8513	0.8252	6.4163	-2.5686	7.5138	0.1066	-1.1936	-0.8442	-0.1401	0.4845	0.9901	0.8872	-1.1539	-0.5911	-0.1121	-0.1479	-0.0112	0.2511	0.1145	0.0268	0.3085	15.7138	72.5422
15	46.1123	-24.139	-8.4275	17.8957	-4.591	16.9504	-0.9598	-1.9469	0.078	0.6596	1.7588	-1.111	-0.1559	-1.0534	-0.799	0.0726	-0.0617	0.1243	0.6121	-0.0898	-0.1699	4.7891	23.1461	79.9562
16	9.4778	6.0219	16.3851	75.3716	13.4715	28.4572	0.6975	-1.7174	-0.6785	2.6251	0.1097	1.1728	0.9704	-0.9059	-0.8072	0.1279	-0.4535	0.2298	0.9155	-0.0312	0.181	1.2155	4.1086	97.9427
17	14.3225	-0.0217	-5.0692	1.865	-5.8191	19.9987	0.5292	-0.5226	0.4747	0.5266	0.0458	0.8035	-0.2259	-0.8826	-0.5749	0.0376	-0.2412	0.1061	0.6068	-0.0496	-0.0303	-0.923	12.5943	104.0806
18	1.4173	-0.1298	0.7386	4.3248	-0.1982	3.6192	-0.0424	-0.4253	-0.3129	0.1218	0.0637	0.0488	0.6341	-0.9989	-0.0214	0.0124	-0.1637	0.0452	0.3843	0.0276	0.0153	9.9467	10.5304	102.0486
19	5.6789	-1.8277	-1.8163	6.2483	-0.0675	7.7714	-0.109	-0.2318	0.1156	0.1754	-0.0313	0.0073	0.0243	-0.2375	0.1404	-0.0021	-0.0167	0.0306	0.2788	-0.0057	0.0617	17.5186	17.8312	94.5935
20	2.2357	-0.783	-0.0102	0.9596	1.5171	8.5045	-0.0462	-0.3065	0.1205	0.1305	0.0075	-0.1413	0.553	0.0723	0.0387	0.0211	0.0054	0.0357	0.1748	0.0337	0.06	24.9282	14.4909	92.4377
21	5.3609	-2.8871	0.9301	5.4557	-1.9144	4.3008	0.0791	0.1325	0.219	-0.0378	-0.0715	-0.3385	-0.0129	0.7099	-0.0076	0.0596	-0.0122	0.0017	0.2753	-0.0246	0.044	31.108	21.0588	91.0589
22	8.8286	-2.6375	1.4146	2.597	-3.0326	13.1262	-0.1309	-0.2674	-0.2616	-0.1254	0.1535	-0.0608	0.4906	0.4009	-0.0226	-0.0274	0.0496	0.0522	0.162	0.0036	0.0545	33.1616	18.8696	81.6855
23	1.0588	1.2291	-0.7938	1.4266	-0.9214	0.5951	0.4238	-0.6512	-0.4699	0.0462	-0.1591	-0.3799	0.2081	0.9246	-0.2647	0.2171	0.0101	-0.0218	0.385	0.0081	0.2347	40.3263	18.8567	74.6296
24	0.9307	0.3555	-2.576	6.2927	0.6799	7.5795	0.0921	0.1509	-0.7496	0.541	0.0826	-0.4701	1.0893	0.5007	-0.1747	0.0777	0.0398	-0.0317	0.1958	-0.0112	0.0226	50.2637	17.905	71.5839
25	0.3902	1.009	1.0799	2.7715	2.4889	3.5562	0.1032	-0.3672	-0.3321	0.3975	-0.0877	0.099	0.6185	0.1931	-0.0155	0.1012	0.0594	-0.0067	0.1999	0.0407	0.0793	44.7479	16.911	62.478
26	16.2321	7.6762	6.1443	3.6939	3.6023	9.9419	0.3064	0.5692	-0.2335	0.3457	0.0956	0.1147	0.5842	0.7771	-0.4021	0.1186	0.1278	0.0257	0.2372	-0.0297	0.0483	50.6765	15.1524	55.0415
27	13.7856	6.7803	1.6829	7.2539	5.4011	5.5424	0.2205	0.1463	-0.1219	0.1349	0.3482	-0.307	0.1607	0.5556	-0.5688	-0.0086	-0.0378	-0.014	0.2866	-0.0462	0.0011	59.602	26.1645	64.3207
28	5.7046	4.9412	1.7306	8.2882	5.1442	3.8401	-0.1143	1.0109	-0.9788	0.5248	1.0249	-1.2566	0.9769	2.3989	-0.9106	-0.0538	0.2111	-0.0796	0.3852	-0.2087	0.1765	62.1096	15.1259	58.0974
29	7.3232	4.4244	7.0905	53.8443	-15.5309	14.5381	-0.0705	1.9345	-0.6163	-2.1107	-0.2029	0.0853	0.6739	-1.3662	0.2734	0.2973	0.0014	0.1282	0.7085	-0.0918	-0.081	56.7243	16.0689	46.598
30	78.2556	25.6046	4.2154	19.9561	23.7303	43.3734	-1.5018	0.5497	2.8893	-1.7347	2.4078	1.3235	-1.7173	0.2871	-0.9061	0.032	-0.0839	0.0823	0.6022	0.1147	0.0035	56.6438	26.1644	49.3482

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 11
2	X-RAY DIFFRACTION	2	A	12 - 61
3	X-RAY DIFFRACTION	3	A	62 - 87
4	X-RAY DIFFRACTION	4	A	88 - 107
5	X-RAY DIFFRACTION	5	A	108 - 118
6	X-RAY DIFFRACTION	6	A	119 - 128
7	X-RAY DIFFRACTION	7	A	129 - 154
8	X-RAY DIFFRACTION	8	A	155 - 168
9	X-RAY DIFFRACTION	9	A	169 - 185
10	X-RAY DIFFRACTION	10	A	186 - 197
11	X-RAY DIFFRACTION	11	A	198 - 204
12	X-RAY DIFFRACTION	12	A	205 - 236
13	X-RAY DIFFRACTION	13	A	237 - 252
14	X-RAY DIFFRACTION	14	A	253 - 275
15	X-RAY DIFFRACTION	15	A	276 - 282
16	X-RAY DIFFRACTION	16	B	0 - 5
17	X-RAY DIFFRACTION	17	B	6 - 17
18	X-RAY DIFFRACTION	18	B	18 - 61
19	X-RAY DIFFRACTION	19	B	62 - 80
20	X-RAY DIFFRACTION	20	B	81 - 107
21	X-RAY DIFFRACTION	21	B	108 - 125
22	X-RAY DIFFRACTION	22	B	126 - 154
23	X-RAY DIFFRACTION	23	B	155 - 188
24	X-RAY DIFFRACTION	24	B	189 - 198
25	X-RAY DIFFRACTION	25	B	199 - 224
26	X-RAY DIFFRACTION	26	B	225 - 243
27	X-RAY DIFFRACTION	27	B	244 - 256
28	X-RAY DIFFRACTION	28	B	257 - 269
29	X-RAY DIFFRACTION	29	B	270 - 276
30	X-RAY DIFFRACTION	30	B	277 - 282

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi