PDB-6e1r: Crystal structure of the Acinetobacter phage vB_ApiP_P1 tailspike...

ID or keywords:

Entry

Database: PDB / ID: 6e1r

Title

Crystal structure of the Acinetobacter phage vB_ApiP_P1 tailspike protein

Components

Tailspike protein

Keywords

HYDROLASE / Acinetobacter phage vB_ApiP_P1 / tailspike / Acinetobacter baumannii

Function / homology

Tailspike protein

Function and homology information

Biological species

Acinetobacter phage vB_ApiP_P1 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.693 Å

Authors

Plattner, M. / Shneider, M.M. / Oliveira, H. / Azeredo, J. / Leiman, P.G.

Citation

Journal: To Be Published
Title: Crystal structure of the Acinetobacter phage vB_ApiP_P1 tailspike protein
Authors: Plattner, M. / Shneider, M.M. / Oliveira, H. / Azeredo, J. / Leiman, P.G.

History

Deposition	Jul 10, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6e1r.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6e1r.ent.gz	1021.5 KB	Display	PDB format
PDBx/mmJSON format	6e1r.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/e1/6e1r ftp://data.pdbj.org/pub/pdb/validation_reports/e1/6e1r	HTTPS FTP

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Related structure data

Similar structure data	3pnd-d 1yc9-1 4bsu-2 1un8-d 6ajg-d 7c2n-d 6ajh-d 4x4v-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: Tailspike protein

B: Tailspike protein

C: Tailspike protein

D: Tailspike protein

E: Tailspike protein

F: Tailspike protein

hetero molecules

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

1

A: Tailspike protein

B: Tailspike protein

C: Tailspike protein

hetero molecules

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

2

D: Tailspike protein

E: Tailspike protein

F: Tailspike protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.123, 90.015, 508.604
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tailspike protein Mass: 59409.586 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter phage vB_ApiP_P1 (virus) / Gene: P1_43 / Plasmid: pTSL / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: A0A221SBY4
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 877 / 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: 2.6 Å³/Da / Density % sol: 52.78 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 100mM sodium Citrate pH 5.5, 2.8M NaCl, 10mM KSCN

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 23, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.69→50 Å / Num. obs: 197955 / % possible obs: 99.4 % / Redundancy: 7.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.16 / R_rim(I) all: 0.173 / Net I/σ(I): 9.93
Reflection shell	Resolution: 2.69→2.86 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.879 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 31287 / CC_1/2: 0.908 / R_rim(I) all: 0.95 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3092: ???)	refinement
XDS		data reduction
SCALA		data scaling
HKL2Map		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.693→49.115 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.8

	R_factor	Num. reflection	% reflection
R_free	0.2375	3641	3.51 %
R_work	0.2001	-	-
obs	0.2015	197326	99.14 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.693→49.115 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24310	0	6	877	25193

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	24772
X-RAY DIFFRACTION	f_angle_d	0.517	33625
X-RAY DIFFRACTION	f_dihedral_angle_d	8.939	14413
X-RAY DIFFRACTION	f_chiral_restr	0.044	3910
X-RAY DIFFRACTION	f_plane_restr	0.003	4313

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 (%)
2.693-2.7236	0.3803	201	0.3498	5608	X-RAY DIFFRACTION	88
2.7236-2.7556	0.3408	231	0.312	6386	X-RAY DIFFRACTION	100
2.7556-2.7892	0.3743	231	0.3	6371	X-RAY DIFFRACTION	100
2.7892-2.8246	0.3523	230	0.2944	6396	X-RAY DIFFRACTION	99
2.8246-2.8617	0.3018	226	0.287	6359	X-RAY DIFFRACTION	100
2.8617-2.9009	0.3198	233	0.2824	6476	X-RAY DIFFRACTION	100
2.9009-2.9424	0.3536	230	0.2736	6279	X-RAY DIFFRACTION	100
2.9424-2.9863	0.3555	234	0.2784	6388	X-RAY DIFFRACTION	100
2.9863-3.0329	0.3533	231	0.275	6326	X-RAY DIFFRACTION	98
3.0329-3.0826	0.3045	225	0.2665	6363	X-RAY DIFFRACTION	99
3.0826-3.1358	0.3052	229	0.2671	6339	X-RAY DIFFRACTION	100
3.1358-3.1928	0.3055	238	0.2472	6432	X-RAY DIFFRACTION	100
3.1928-3.2542	0.2524	237	0.2285	6376	X-RAY DIFFRACTION	100
3.2542-3.3206	0.3095	234	0.2286	6357	X-RAY DIFFRACTION	100
3.3206-3.3928	0.2409	238	0.2171	6419	X-RAY DIFFRACTION	100
3.3928-3.4717	0.2223	237	0.2088	6407	X-RAY DIFFRACTION	100
3.4717-3.5585	0.2563	235	0.1984	6419	X-RAY DIFFRACTION	100
3.5585-3.6547	0.2602	228	0.1925	6402	X-RAY DIFFRACTION	100
3.6547-3.7622	0.2268	224	0.1817	6361	X-RAY DIFFRACTION	100
3.7622-3.8836	0.225	229	0.1725	6417	X-RAY DIFFRACTION	100
3.8836-4.0223	0.2067	236	0.1716	6397	X-RAY DIFFRACTION	100
4.0223-4.1833	0.204	232	0.1629	6344	X-RAY DIFFRACTION	100
4.1833-4.3735	0.1621	234	0.1423	6359	X-RAY DIFFRACTION	100
4.3735-4.604	0.1689	229	0.1373	6349	X-RAY DIFFRACTION	99
4.604-4.8922	0.1917	235	0.1346	6304	X-RAY DIFFRACTION	98
4.8922-5.2695	0.1921	229	0.153	6401	X-RAY DIFFRACTION	100
5.2695-5.799	0.1983	234	0.1708	6358	X-RAY DIFFRACTION	99
5.799-6.6364	0.1817	231	0.1668	6297	X-RAY DIFFRACTION	99
6.6364-8.3545	0.1908	237	0.1831	6388	X-RAY DIFFRACTION	100
8.3545-49.1235	0.2013	230	0.2034	6320	X-RAY DIFFRACTION	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	4.3509	1.0167	1.5395	4.8699	2.4884	2.4778	-0.2277	-0.4287	-0.0441	0.7334	0.252	-0.0843	0.0425	-0.2296	-0.0398	0.8499	0.093	0.0542	0.717	-0.0212	0.3778	-16.853	15.2999	-43.7565
2	1.1703	-0.0724	1.1452	0.8413	0.1845	3.7707	-0.0648	-0.2593	0.1054	0.2211	0.02	-0.0082	-0.2183	-0.1186	0.0443	0.3816	-0.0054	0.0189	0.3114	-0.0214	0.3317	-24.6592	19.6771	-81.0069
3	0.1121	-0.0409	-0.3248	0.0338	-0.1239	1.9182	0.0328	-0.045	-0.0293	-0.0227	-0.0187	0.0258	-0.1252	-0.0533	-0.0127	0.3493	-0.0042	-0.0169	0.3398	-0.0165	0.34	-22.0913	13.4709	-130.7518
4	0.6197	-0.135	0.4744	1.2488	0.8331	2.5274	-0.0448	-0.2997	-0.0699	0.4248	-0.0218	0.2134	0.068	-0.3282	0.0689	0.574	-0.0057	0.15	0.6438	0.0496	0.4596	-34.8021	-3.9147	-61.5801
5	0.035	-0.1037	0.1059	0.0414	-0.1123	2.1922	0.0496	0.0256	-0.0176	-0.0428	-0.0281	0.0563	0.1573	-0.0437	-0.031	0.2716	-0.0195	0.0091	0.317	-0.0355	0.3644	-30.6219	-8.5658	-115.7006
6	1.5157	0.0769	-0.8581	0.9405	0.0316	3.6933	-0.1014	-0.3422	-0.1215	0.5315	0.0496	-0.0609	0.1799	0.0948	0.0422	0.6654	0.044	-0.0319	0.4802	0.0336	0.381	-9.3593	-5.3345	-57.5304
7	0.0354	-0.0079	0.1026	0.2738	0.2027	1.5718	0.0298	0.0217	-0.003	0.0539	-0.0193	-0.0327	-0.0086	0.2474	-0.015	0.2405	0.0045	-0.0047	0.3773	0.0262	0.3268	-6.0462	-2.0906	-111.79
8	5.2684	-0.3139	0.4054	0.6625	0.0207	7.2383	0.6282	-0.8306	0.4222	0.2019	-0.2125	0.0647	-1.0805	0.1235	-0.3934	2.4383	0.1806	0.1408	1.4124	0.0422	0.588	8.5055	34.1964	16.3665
9	0.6412	0.0966	0.586	0.3838	-0.0581	0.5922	0.2267	-0.5401	-0.0319	0.2894	-0.1013	0.1051	0.0956	-0.1778	-0.1022	2.0742	0.1568	0.1942	1.2429	0.116	0.491	8.0438	30.3107	-0.2718
10	0.6591	0.2733	-0.2605	0.1573	-0.2957	2.7088	-0.0853	-0.3965	-0.1827	0.8426	0.1552	0.031	0.1073	-0.1428	-0.0657	1.3187	0.1285	0.032	0.693	0.1001	0.4736	16.2336	26.8086	-31.417
11	0.7373	-0.3494	-0.395	2.1045	-0.119	1.0099	-0.2477	-0.0949	-0.0775	0.3178	0.1249	0.0592	0.0725	0.0019	0.089	0.3856	0.005	0.0483	0.3673	0.0287	0.3157	15.7796	35.6576	-70.4184
12	2.6294	-1.6021	-0.5544	1.1936	0.4618	1.0904	0.0299	0.0463	-0.0765	0.1639	-0.0765	0.0158	0.1913	-0.1348	0.0448	0.4094	-0.0758	0.0091	0.3521	0.0093	0.357	11.8501	32.7933	-88.3729
13	0.0004	-0.0198	-0.0124	0.2349	0.1509	0.0945	-0.1122	0.0907	0.0359	0.227	0.0628	-0.0038	-0.155	0.2926	0.088	2.7126	0.3898	-0.2179	1.3214	0.0352	0.6493	26.95	40.0097	17.0634
14	0.256	0.0047	0.3698	-0.0027	0.0035	0.5604	-0.1561	-0.3977	0.1656	0.9545	0.1316	-0.5376	-0.3569	0.298	0.2211	1.7408	0.1352	-0.5134	0.86	-0.0635	0.5377	33.2354	49.0046	-23.3825
15	1.5402	-0.1306	-0.919	0.9462	0.335	1.876	-0.0187	-0.0537	0.1342	0.5355	-0.0864	-0.3272	-0.4699	-0.0017	0.1444	0.8275	0.0783	-0.092	0.4965	0.0242	0.4279	22.6091	52.0911	-61.3894
16	3.1162	1.1665	0.9709	5.0162	0.2989	2.6674	-0.1092	-0.08	-0.0166	0.0721	0.0254	-0.248	-0.0284	0.1526	0.0882	0.2554	0.0108	0.0188	0.3131	0.0061	0.2729	34.3446	43.5252	-86.5019
17	2.1521	0.5734	-1.425	1.0619	1.0303	4.7901	0.1239	-0.5272	-0.0444	0.2469	0.1547	-0.1456	0.3451	-0.3999	-0.2266	2.3408	0.3546	-0.1733	1.2835	-0.0771	0.5866	13.2966	54.3294	14.9446
18	0.6938	0.6736	1.5938	1.4824	1.7376	3.7089	-0.0115	-0.2408	0.1268	0.6069	-0.0232	0.2139	-0.4337	-0.3529	0.2512	1.9084	0.2656	-0.0639	1.2198	-0.0703	0.4676	7.0829	57.9969	-2.6019
19	0.3374	0.187	0.1679	0.1401	-0.1263	1.4724	0.0355	-0.1755	0.1075	0.2971	-0.0301	0.0905	-0.2405	-0.3833	0.0682	2.0429	0.3731	0.0686	1.0366	-0.0577	0.5082	5.8021	56.7301	-14.215
20	0.571	0.3984	0.9865	0.6601	0.2973	3.2618	0.0623	-0.1774	0.0634	0.6292	-0.027	0.1508	-0.043	-0.915	-0.0609	1.7969	0.3486	0.1301	1.0315	0.0295	0.5007	2.2238	52.3488	-20.8003
21	1.5634	-0.8567	-0.8768	1.8322	2.0969	2.4232	-0.069	-0.3436	0.1588	1.0038	0.1554	0.1895	-0.6098	-0.5038	-0.0268	1.2995	0.3293	0.0912	0.7737	0.0305	0.4863	3.4768	54.1977	-34.6536
22	4.0312	-0.7524	-3.0807	2.1351	0.5281	5.2205	-0.2324	-0.3097	0.0408	0.4737	0.2525	0.0593	-0.2744	-0.5708	-0.0441	0.6794	0.11	-0.0485	0.5613	0.0255	0.3538	6.8817	47.1102	-55.1831
23	3.2728	0.201	0.6816	0.2358	0.4362	1.2057	0.0575	-0.039	0.0804	0.1419	-0.0581	0.0064	0.0109	-0.1162	-0.0031	0.3961	-0.0026	-0.01	0.2972	0.04	0.3399	13.0471	59.0172	-86.683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 206 through 276 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 277 through 542 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 543 through 749 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 207 through 423 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 424 through 749 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 206 through 391 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 392 through 749 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 206 through 252 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 253 through 332 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 333 through 590 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 591 through 659 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 660 through 749 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 206 through 252 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 253 through 590 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 591 through 630 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 631 through 749 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 206 through 276 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 277 through 324 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 325 through 391 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 392 through 423 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 424 through 545 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 546 through 630 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 631 through 749 )

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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

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Open data

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Basic information

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi