PDB-3spe: Crystal structure of the tail sheath protein protease resistant f...

ID or keywords:

Entry

Database: PDB / ID: 3spe

Title

Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ

Components

PHIKZ029

Keywords

STRUCTURAL PROTEIN

Function / homology

: / Bacteriophage phiKZ, gp29PR /

PHOSPHATE ION / PHIKZ029

Function and homology information

Biological species

Pseudomonas phage phiKZ (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3996 Å

Authors

Aksyuk, A.A. / Kurochkina, L.P. / Fokine, A. / Mesyanzhinov, V.V. / Rossmann, M.G.

Citation

Journal: Structure / Year: 2011
Title: Structural conservation of the myoviridae phage tail sheath protein fold.
Authors: Anastasia A Aksyuk / Lidia P Kurochkina / Andrei Fokine / Farhad Forouhar / Vadim V Mesyanzhinov / Liang Tong / Michael G Rossmann /

Abstract: Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The ...

History

Deposition	Jul 1, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 14, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 28, 2011	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3spe.cif.gz	209.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3spe.ent.gz	176.4 KB	Display	PDB format
PDBx/mmJSON format	3spe.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/sp/3spe ftp://data.pdbj.org/pub/pdb/validation_reports/sp/3spe	HTTPS FTP

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Related structure data

Related structure data	5331C 5332C 3j0hC 3j0iC 3hxl 3lml C: citing same article (ref.)
Similar structure data	4huo-d 7new-1 4qua-d 4ucc-2 4mx5-d 4hup-d 3srp-d 6g05-1 5ntn-2 5yp6-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: PHIKZ029

B: PHIKZ029

hetero molecules

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

1

A: PHIKZ029

hetero molecules

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

2

B: PHIKZ029

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	70.892, 156.715, 61.003
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain B and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	B	147 - 177
1	2	1	chain B and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	B	184 - 214
1	3	1	chain B and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	B	219 - 238
1	4	1	chain B and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	B	247 - 287
1	5	1	chain B and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	B	300 - 350
2	1	1	chain A and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	A	147 - 177
2	2	1	chain A and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	A	184 - 214
2	3	1	chain A and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	A	219 - 238
2	4	1	chain A and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	A	247 - 287
2	5	1	chain A and (resid 147:177 or resid 184:214 or resid 219:238 or resid 247:287 or resid 300:350)	A	300 - 350

Details

This structure is a protease resistant fragment, gp29PR, that is a part of a larger full length protein gp29 (this structure is 96-390 out of 1-695). The dimer surface between monomers forming the crystal dimer (identified by PISA) would be not available for interaction in the full length gp29 protein. Therefore, the full length protein cannot form a similar dimer due to steric clashes. So this dimer seems to be an artifact present only for the smaller fragment, gp29PR, and is not biologically relevant.

#1: Protein	PHIKZ029 Mass: 32531.383 Da / Num. of mol.: 2 Fragment: Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Gene: bacteriophage phiKZ, gene product 29, ORF029 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SDD3
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.58 Å³/Da / Density % sol: 52.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97948, 0.97962, 0.94949

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 7, 2010

Radiation

Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97948	1
2	0.97962	1
3	0.94949	1

Reflection

Resolution: 2.3996→30 Å / Num. all: 27334 / Num. obs: 26951 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / R_merge(I) obs: 0.107

Reflection shell

Resolution (Å)	R_merge(I) obs	Diffraction-ID	% possible all
2.3996-2.49	0.646	1	99.7
5.16-30	0.059	1	99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
SHELXCD		phasing
SHELXE		model building
RESOLVE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.3996→28.424 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7531 / SU ML: 0.44 / σ(F): 1.89 / Phase error: 31 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2865	2534	5.02 %	RANDOM
R_work	0.256	-	-	-
obs	0.2579	26888	98.23 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 35.008 Å² / k_sol: 0.339 e/Å³

Displacement parameters

B_iso max: 276.91 Å² / B_iso mean: 44.6903 Å² / B_iso min: 7.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.0725 Å²	-0 Å²	0 Å²
2-	-	-8.4414 Å²	-0 Å²
3-	-	-	3.3689 Å²

Refinement step

Cycle: LAST / Resolution: 2.3996→28.424 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3895	0	16	99	4010

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4037
X-RAY DIFFRACTION	f_angle_d	1.294	5492
X-RAY DIFFRACTION	f_chiral_restr	0.089	626
X-RAY DIFFRACTION	f_plane_restr	0.005	717
X-RAY DIFFRACTION	f_dihedral_angle_d	15.131	1461

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	B	1376	X-RAY DIFFRACTION	POSITIONAL	0.043
1	2	A	1376	X-RAY DIFFRACTION	POSITIONAL	0.043

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3996-2.4457	0.417	130	0.3924	2627	2757	96
2.4457-2.4956	0.5158	173	0.393	2603	2776	100
2.4956-2.5498	0.406	127	0.3643	2774	2901	100
2.5498-2.6091	0.4207	141	0.3334	2696	2837	100
2.6091-2.6743	0.4132	164	0.3422	2691	2855	100
2.6743-2.7466	0.3798	134	0.3091	2728	2862	100
2.7466-2.8273	0.2861	133	0.293	2697	2830	100
2.8273-2.9185	0.3179	134	0.2948	2733	2867	100
2.9185-3.0227	0.3433	139	0.2872	2706	2845	100
3.0227-3.1435	0.272	153	0.282	2704	2857	100
3.1435-3.2864	0.2687	136	0.2558	2690	2826	100
3.2864-3.4594	0.3183	148	0.2465	2704	2852	100
3.4594-3.6757	0.3148	137	0.2632	2314	2451	86
3.6757-3.9588	0.261	95	0.2304	2415	2510	88
3.9588-4.356	0.2518	152	0.1919	2710	2862	100
4.356-4.9833	0.1988	150	0.169	2707	2857	100
4.9833-6.2674	0.2452	152	0.1993	2702	2854	100
6.2674-28.4259	0.2064	136	0.2008	2705	2841	99

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	0.6023	0.3934	-0.0432	0.2909	0.2088	0.3643	-0.1212	0.0244	-0.1478	-0.1007	0.025	-0.0534	0.1275	0.1505	-0.1017	0.1435	0.0575	0.0182	0.1251	0.0335	0.0802	-9.5878	-39.7778	-48.4362
2	0.6097	0.3598	0.4401	0.752	-0.2414	0.781	-0.2078	-0.4589	0.5178	0.3602	-0.3294	0.4281	-0.3599	0.0479	-0.5623	0.049	-0.0478	0.0726	-0.0289	0.0663	-0.0898	-11.3265	-34.1068	-49.7955
3	0.1305	0.0838	-0.0037	0.1466	-0.0494	0.177	0.0707	-0.1045	0.1265	0.3047	0.0323	0.0456	0.0855	0.152	0.2371	0.8533	0.3142	0.3603	0.4841	0.3167	0.5319	-21.2267	-38.111	-25.8927
4	0.7139	0.4271	0.2959	1.1531	-0.0968	0.4283	-0.3382	-0.172	-0.1796	0.3312	0.1874	-0.2536	-0.2295	0.1044	0.0419	0.3643	-0.0176	0.0041	0.308	0.0507	0.2639	-11.363	-25.9392	-35.7633
5	1.2497	0.2216	-0.243	0.9676	-0.2508	0.0879	-0.0819	-1.0849	0.0453	0.7293	0.1946	0.3149	-0.1048	-0.0189	0.056	0.3295	0.116	0.0989	0.4301	0.0288	0.1215	-23.3581	-27.2758	-32.1435
6	0.233	-0.0419	0.2186	0.1747	-0.0354	0.2168	-0.151	-0.1403	-0.2088	0.0085	0.111	0.3141	-0.0172	-0.1172	0.0218	0.3639	0.0789	0.1957	0.202	0.0559	0.3128	-26.359	-26.2074	-36.3011
7	1.2292	0.1455	-0.7228	0.5967	-0.7863	1.393	0.3612	-0.314	0.4504	0.5542	-0.0369	0.0819	-0.9136	0.1046	-0.1369	0.0886	0.1883	0.1724	0.1697	0.0624	0.3623	-23.9651	-17.3866	-41.5942
8	0.0784	-0.1213	-0.0165	0.1692	-0.0099	-0.0109	-0.245	-0.1476	-0.3718	0.1591	-0.021	-0.1206	0.2035	0.0195	0.051	0.2877	0.0178	0.0897	0.1611	0.0641	0.3623	-18.4912	-48.8258	-42.6903
9	0.3908	-0.1348	-0.2719	0.0592	0.105	0.4245	-0.4999	-0.4218	-0.9157	0.5752	0.1763	-0.1122	0.4637	0.1033	-0.1983	0.5404	0.0963	0.0634	0.2874	0.2095	0.2354	-12.0077	-46.1653	-35.298
10	0.8863	-0.0622	-0.3682	0.0333	0.0091	0.9898	-0.1272	-0.3479	-0.2023	-0.2437	0.3119	-0.1127	0.1321	0.259	0.0816	0.2337	-0.0567	0.0085	0.1031	-0.0546	0.0358	-6.974	-26.47	-44.8931
11	1.2907	0.3075	-0.1976	0.337	-0.0773	0.9221	0.1294	-0.482	0.3604	0.1734	0.0934	0.079	-0.174	-0.0009	0.2093	0.0985	-0.0058	0.0037	0.0665	0.0451	0.1164	-13.8214	13.0447	-41.5279
12	0.4113	0.1093	0.0301	0.5909	-0.1746	0.0646	-0.1499	-0.0101	0.2837	-0.1694	0.061	-0.0625	-0.2339	0.2673	-0.0414	0.338	-0.2687	-0.0776	0.3134	-0.0632	0.1457	-9.3842	24.8986	-48.9602
13	1.0073	0.2967	-0.1478	0.3816	-0.0505	0.106	0.1747	-0.4621	0.1377	0.3956	-0.2291	0.1472	-0.1495	0.5031	0.0179	0.646	-0.1485	0.0859	0.3733	0.0098	0.3015	-14.6283	15.6131	-35.6306
14	0.7659	0.1937	-0.4553	1.5081	0.4868	0.5492	-0.1901	0.0299	-0.5282	0.8148	-0.1531	-0.1985	0.3045	0.5013	-0.3248	0.3149	-0.1082	0.0749	0.0288	-0.0444	0.3663	-15.193	1.5099	-45.0525
15	0.3888	0.3624	0.0499	1.8649	-0.411	0.6626	-0.0226	0.1919	-0.046	-0.2676	-0.1061	-0.6124	-0.0924	0.7186	0.1346	0.0154	-0.3102	0.1115	0.1674	0.1372	0.0529	-23.9226	12.5047	-65.8694
16	0.2364	-0.0599	-0.111	0.6883	0.0439	0.5769	0.0896	-0.2296	-0.4055	0.1881	0.3789	-0.6414	0.7596	0.64	0.7109	-0.798	-0.1642	0.4063	0.2436	0.0261	0.2717	-12.9285	0.9905	-55.4106
17	0.2579	0.127	0.18	0.2365	0.1813	0.1347	-0.5746	0.5043	0.0272	-0.4066	0.098	0.2058	0.0247	-0.0465	-0.7248	-0.3942	-0.7004	0.3109	0.138	0.008	0.3292	-24.8269	1.4668	-59.7657
18	0.8194	-0.3392	0.5375	0.3379	0.1135	0.9861	-0.1963	-0.019	0.3279	-0.2877	0.2003	0.798	-0.0337	-0.3757	0.0352	0.1771	-0.1089	-0.0575	0.2344	0.0121	0.3201	-27.7988	0.0632	-55.6839
19	0.7459	-0.3744	0.7795	0.1926	-0.3831	0.7538	0.3557	-0.0591	-0.2563	-0.2984	-0.0916	0.0052	0.2878	-0.0083	-0.0868	0.294	-0.0607	-0.0092	0.1604	0.0202	0.2537	-24.4862	-8.4595	-50.0117
20	1.0023	0.0361	0.1195	0.2121	0.175	0.4946	-0.2319	-0.4348	0.2217	0.2443	0.0611	0.2049	0.0802	0.0007	-0.1539	0.0823	-0.0367	0.0295	0.0877	-0.0182	0.2165	-22.6734	23.4076	-49.0913
21	0.1177	0.0544	-0.061	0.0306	-0.012	0.0369	-0.2877	0.203	0.4274	-0.1842	0.0975	-0.1584	0.1938	0.0511	-0.118	0.162	-0.1401	0.0224	0.0166	0.1197	0.1694	-15.7542	21.4943	-56.2655
22	0.6296	-0.5193	-0.1336	1.3804	0.7438	1.0313	-0.0464	-0.076	-0.4087	0.3956	0.4038	-0.3387	0.1484	0.3451	0.0222	0.1239	0.0089	-0.016	0.2233	-0.0483	0.3884	-8.621	2.4922	-46.8491

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 102:167)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 168:210)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 211:227)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 228:248)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 249:270)	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 271:285)	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 286:307)	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 308:325)	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 326:362)	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 363:381)	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 103:117)	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 118:157)	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 158:184)	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 185:210)	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 211:227)	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 228:248)	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 249:270)	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 271:285)	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 286:307)	B
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 308:325)	B
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 326:362)	B
22	X-RAY DIFFRACTION	22	chain 'B' and (resseq 363:381)	B

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