PDB-5w6p: Crystal structure of Bacteriophage CBA120 tailspike protein 2 enz...

ID or keywords:

Entry

Database: PDB / ID: 5w6p

Title

Crystal structure of Bacteriophage CBA120 tailspike protein 2 enzymatically active domain (TSP2dN, orf211)

Components

tailspike protein 2

Keywords

viral protein / hydrolase / CBA120 / tailspikes

Function / homology

metal ion binding / : / Putative tail fiber

Function and homology information

Biological species

Escherichia phage Cba120 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.335 Å

Authors

Plattner, M. / Shneider, M.M. / Leiman, P.G.

Funding support

Switzerland, 1items

Citation

Journal: J.Mol.Biol. / Year: 2019
Title: Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120.
Authors: Plattner, M. / Shneider, M.M. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Nazarov, S. / Prokhorov, N.S. / Taylor, N.M.I. / Buth, S.A. / Gambino, M. / Gencay, Y.E. / Brondsted, L. / ...

History

Deposition	Jun 16, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2019	Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2	Nov 6, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Dec 2, 2020	Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5w6p.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb5w6p.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	5w6p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5w6p_validation.pdf.gz	498.3 KB	Display	wwPDB validaton report
Full document	5w6p_full_validation.pdf.gz	530.3 KB	Display
Data in XML	5w6p_validation.xml.gz	150.9 KB	Display
Data in CIF	5w6p_validation.cif.gz	218.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/5w6p ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w6p	HTTPS FTP

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Related structure data

Related structure data	5w6fC 5w6hC 5w6sC C: citing same article (ref.)
Similar structure data	5w6s-1 4e7l-1 1cvi-d 11223 4bxh-3 6td3-2 4e7k-1 3e3l-1 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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: tailspike protein 2

B: tailspike protein 2

C: tailspike protein 2

D: tailspike protein 2

E: tailspike protein 2

F: tailspike protein 2

hetero molecules

436 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: tailspike protein 2

B: tailspike protein 2

C: tailspike protein 2

hetero molecules

defined by author&software
Evidence: gel filtration, Homo Trimer
218 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: tailspike protein 2

E: tailspike protein 2

F: tailspike protein 2

hetero molecules

defined by author&software
218 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.519, 303.227, 113.207
Angle α, β, γ (deg.)	90.00, 90.38, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-1001- ZN
2	1	D-1004- ZN
3	1	B-1141- HOH

#1: Protein	tailspike protein 2 Mass: 72143.117 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage Cba120 (virus) / Gene: orf211 / Production host: Escherichia coli B (bacteria) / Strain (production host): 834 / References: UniProt: G3M190
#2: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1981 / 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: 2.75 Å³/Da / Density % sol: 55.21 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 16% PEG 8000, 100mM Zinc Acetate, 100mM Tris HCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.33→50 Å / Num. obs: 385363 / % possible obs: 98.5 % / Redundancy: 3.5 % / Net I/σ(I): 10.48

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2666: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.335→46.683 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 20.29

	R_factor	Num. reflection	% reflection
R_free	0.1896	19276	5 %
R_work	0.154	-	-
obs	0.1558	385228	98.44 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.335→46.683 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30340	0	66	1981	32387

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	30954
X-RAY DIFFRACTION	f_angle_d	0.719	42111
X-RAY DIFFRACTION	f_dihedral_angle_d	13.833	17967
X-RAY DIFFRACTION	f_chiral_restr	0.053	4811
X-RAY DIFFRACTION	f_plane_restr	0.004	5534

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 (%)
2.3348-2.3613	0.3317	590	0.2761	11217	X-RAY DIFFRACTION	90
2.3613-2.3891	0.2778	644	0.246	12245	X-RAY DIFFRACTION	99
2.3891-2.4182	0.2659	649	0.2225	12344	X-RAY DIFFRACTION	99
2.4182-2.4488	0.2667	648	0.2191	12289	X-RAY DIFFRACTION	99
2.4488-2.481	0.2671	644	0.2073	12253	X-RAY DIFFRACTION	99
2.481-2.515	0.2386	650	0.1923	12329	X-RAY DIFFRACTION	99
2.515-2.5509	0.232	642	0.189	12201	X-RAY DIFFRACTION	99
2.5509-2.589	0.2542	648	0.1981	12316	X-RAY DIFFRACTION	99
2.589-2.6295	0.2365	652	0.1861	12307	X-RAY DIFFRACTION	99
2.6295-2.6726	0.2495	643	0.1869	12180	X-RAY DIFFRACTION	99
2.6726-2.7187	0.2398	643	0.1876	12225	X-RAY DIFFRACTION	99
2.7187-2.7681	0.2338	642	0.1815	12157	X-RAY DIFFRACTION	98
2.7681-2.8213	0.2059	620	0.1719	11884	X-RAY DIFFRACTION	96
2.8213-2.8789	0.2044	646	0.1727	12265	X-RAY DIFFRACTION	99
2.8789-2.9415	0.2206	646	0.1743	12283	X-RAY DIFFRACTION	99
2.9415-3.0099	0.2258	646	0.1741	12319	X-RAY DIFFRACTION	99
3.0099-3.0852	0.2164	649	0.1704	12323	X-RAY DIFFRACTION	99
3.0852-3.1686	0.2091	645	0.1695	12202	X-RAY DIFFRACTION	99
3.1686-3.2618	0.2054	653	0.1707	12399	X-RAY DIFFRACTION	99
3.2618-3.367	0.2134	641	0.1697	12161	X-RAY DIFFRACTION	99
3.367-3.4873	0.1897	648	0.1634	12331	X-RAY DIFFRACTION	99
3.4873-3.6269	0.1855	635	0.1481	12118	X-RAY DIFFRACTION	98
3.6269-3.7919	0.1831	642	0.1418	12122	X-RAY DIFFRACTION	97
3.7919-3.9917	0.1691	647	0.1365	12224	X-RAY DIFFRACTION	99
3.9917-4.2417	0.1533	648	0.1211	12288	X-RAY DIFFRACTION	99
4.2417-4.5689	0.1286	648	0.1018	12310	X-RAY DIFFRACTION	99
4.5689-5.0282	0.1196	649	0.1025	12228	X-RAY DIFFRACTION	98
5.0282-5.7547	0.1609	630	0.1274	12036	X-RAY DIFFRACTION	97
5.7547-7.2459	0.1629	644	0.1351	12255	X-RAY DIFFRACTION	99
7.2459-46.6927	0.1577	644	0.1427	12141	X-RAY DIFFRACTION	98

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	1.9391	0.1007	0.4207	2.3041	-1.6543	3.5159	-0.236	0.0843	0.3836	-0.4067	0.2312	0.1165	-0.7735	-0.1172	0.051	0.8135	-0.0552	-0.022	0.3511	-0.108	0.512	306.2634	76.9965	157.4249
2	1.439	-1.0713	-0.6215	1.7389	-0.1449	2.3279	0.136	-0.0005	0.0828	0.0203	-0.0557	0.0307	-0.4513	0.2978	-0.0513	0.5532	-0.0451	0.0396	0.3131	-0.1003	0.3902	309.7883	61.634	164.3313
3	0.2598	-0.0997	-0.0743	1.1881	0.4306	0.6998	-0.0325	-0.1033	0.0016	0.0302	0.0966	-0.1669	0.0524	0.0855	-0.0766	0.2559	-0.0119	-0.0162	0.3492	-0.0372	0.3043	317.4798	15.4084	146.7531
4	0.797	-0.2343	0.0128	1.192	-0.3719	1.416	-0.0023	0.0408	-0.0534	-0.2274	0.0647	-0.1677	0.0869	0.1597	-0.0713	0.467	-0.0381	0.0147	0.3072	-0.0597	0.3636	316.634	-10.3591	123.7173
5	3.8648	2.7281	0.044	4.4855	-0.2023	1.2501	-0.1039	-0.0393	0.5892	0.1849	0.1436	0.559	-0.4612	-0.0411	-0.0396	0.6379	0.0896	-0.0198	0.3092	-0.0383	0.3758	291.4923	69.7205	155.7548
6	0.2993	-0.271	-0.0733	1.2407	-0.1356	0.5024	-0.0684	-0.1409	-0.0651	0.1765	0.0723	0.0323	0.1328	-0.0397	-0.0067	0.33	-0.0067	-0.0002	0.3777	0.0237	0.2608	298.0288	5.8336	163.1504
7	1.8662	-0.0324	0.1896	5.1959	1.9659	1.8043	-0.2831	0.0236	0.3225	-0.5681	0.3733	-0.0511	-0.785	0.2789	-0.188	0.7706	-0.0759	0.0049	0.3741	-0.0658	0.4392	304.3963	71.0504	144.1121
8	0.3103	0.159	-0.0355	0.8743	0.1408	0.5153	0.0193	-0.0277	-0.0499	-0.1111	-0.0282	0.1291	0.0533	-0.1334	0.0029	0.2673	-0.0391	-0.0475	0.3321	-0.0033	0.2727	287.8195	9.1786	135.3363
9	2.9462	2.1506	0.2611	4.6355	0.0372	1.072	-0.0894	0.1244	-0.4267	0.0229	0.0809	-0.7446	0.2595	0.0391	0.026	0.6319	0.0128	0.1581	0.3317	-0.0177	0.5337	331.2678	13.5131	213.3633
10	0.7544	-0.4688	0.1832	1.6288	0.7472	1.2236	-0.0382	-0.0637	-0.0715	0.0374	0.0224	-0.1327	0.1518	0.0022	0.0324	0.4067	0.0244	0.0822	0.3295	0.0412	0.3858	334.5777	41.7952	219.3043
11	2.5464	-0.1859	-1.7793	2.8168	0.7628	4.1487	0.0693	0.0275	-0.0103	-0.1257	-0.0305	-0.2486	-0.0132	0.0294	-0.0361	0.3418	0.0246	0.0605	0.2808	0.0391	0.3652	336.5877	51.6212	210.1731
12	0.2861	-0.249	0.0049	1.2072	0.0049	0.5033	-0.0299	-0.0669	0.0907	0.105	-0.0108	-0.0285	-0.1778	-0.0972	0.0472	0.3929	0.0676	0.0165	0.322	-0.0298	0.3022	318.5261	89.204	221.7227
13	1.8782	-0.1246	-1.5978	2.042	1.9968	5.0482	-0.1486	0.1971	-0.1671	-0.2174	0.2021	0.0227	0.4561	0.064	-0.0166	0.6533	-0.0769	0.1051	0.3737	0.0395	0.5138	316.5494	5.9411	214.5067
14	1.1233	-1.1373	0.2365	1.2503	-0.5295	3.1046	0.1059	-0.0227	0.0133	-0.0308	0.0543	0.0618	0.154	-0.2206	-0.1302	0.5577	-0.0597	0.0933	0.2878	0.0265	0.4285	312.553	21.2029	221.1003
15	0.5161	0.0292	0.3892	0.6912	-0.1675	1.0207	-0.081	-0.0725	-0.0928	-0.0507	0.0734	0.1049	0.1708	-0.1955	0.0116	0.4227	-0.0212	0.0779	0.4208	0.0461	0.3579	306.0649	44.3791	214.5732
16	2.6606	1.0582	1.7654	2.4791	0.065	1.9569	-0.0631	0.0764	-0.1057	-0.1753	0.114	0.185	0.0459	-0.0455	-0.0757	0.3514	0.0068	0.0695	0.3584	0.034	0.2796	302.4072	60.8445	206.485
17	1.8925	0.4451	1.7695	1.4856	-0.3479	2.1101	-0.0664	0.0051	0.0375	-0.0412	0.0333	0.0713	-0.0666	-0.2058	0.0261	0.3108	0.03	0.0419	0.3532	0.0056	0.2519	304.7579	72.1806	203.5025
18	0.4402	0.043	-0.2198	1.4904	-0.6816	0.913	-0.0778	0.1137	0.1273	-0.2381	0.1162	0.1029	-0.0573	-0.29	-0.0382	0.4562	0.05	-0.0043	0.3908	0.0401	0.3404	303.8968	93.4195	184.0159
19	1.5176	-0.018	-0.195	1.2862	-0.211	1.579	-0.0373	0.0862	0.0569	-0.1592	0.0708	0.0468	-0.1199	-0.3267	-0.0334	0.5145	0.047	0.0318	0.3396	0.0368	0.3345	306.0214	93.5138	183.5329
20	0.8651	-0.6231	0.6551	5.2254	-2.9009	2.9007	-0.0706	0.1514	-0.1184	-0.9754	0.2227	-0.0696	0.6554	-0.1654	-0.1259	0.8107	-0.1369	0.1234	0.4085	0.004	0.4774	318.9705	11.8514	201.1875
21	0.2829	0.1508	-0.0464	0.8881	-0.1004	0.4738	-0.0065	0.0219	0.0471	-0.1915	-0.0251	-0.2076	-0.0125	-0.0026	0.0279	0.4339	0.0278	0.1083	0.342	0.0142	0.4014	334.4683	74.085	192.9262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 246 through 287 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 288 through 335 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 336 through 762 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 763 through 921 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 246 through 335 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 336 through 921 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 246 through 335 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 336 through 921 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 246 through 335 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 336 through 444 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 445 through 493 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 494 through 921 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 246 through 287 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 288 through 335 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 336 through 493 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 494 through 553 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 554 through 622 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 623 through 803 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 804 through 921 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 246 through 335 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 336 through 921 )

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Yorodumi