PDB-4k6b: Atomic structure of bacteriophage HS1 tail needle knob

ID or keywords:

Entry

Database: PDB / ID: 4k6b

Title

Atomic structure of bacteriophage HS1 tail needle knob

Components

HS1 knob domain

Keywords

VIRAL PROTEIN / Jelly-roll topology / Cell membrane penetration / Viral infection

Function / homology

Sf6-type phage tail needle knob / Jelly Rolls / Sandwich / Mainly Beta / GLUTAMIC ACID / PHOSPHATE ION

Function and homology information

Biological species

unidentified phage (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.101 Å

Authors

Bhardwaj, A. / Cingolani, G.

Citation

Journal: Plos One / Year: 2013
Title: The tip of the tail needle affects the rate of DNA delivery by bacteriophage p22.
Authors: Leavitt, J.C. / Gogokhia, L. / Gilcrease, E.B. / Bhardwaj, A. / Cingolani, G. / Casjens, S.R.

History

Deposition	Apr 15, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 28, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4k6b.cif.gz	267.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4k6b.ent.gz	221.5 KB	Display	PDB format
PDBx/mmJSON format	4k6b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4k6b_validation.pdf.gz	456.8 KB	Display	wwPDB validaton report
Full document	4k6b_full_validation.pdf.gz	457.4 KB	Display
Data in XML	4k6b_validation.xml.gz	26.5 KB	Display
Data in CIF	4k6b_validation.cif.gz	41.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k6/4k6b ftp://data.pdbj.org/pub/pdb/validation_reports/k6/4k6b	HTTPS FTP

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Related structure data

Related structure data	3fxf PDB Unreleased entry 3rwn
Similar structure data	3rwn-d 6ki1-2 5bz2-d 6q5r-d 5ah1-d 4z29-d 3vur-1 6x82-1 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
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: HS1 knob domain

B: HS1 knob domain

C: HS1 knob domain

hetero molecules

51.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.780, 87.363, 88.849
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	HS1 knob domain Mass: 17096.293 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified phage (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	HS1 HAS BEEN IDENTIFIED AS 'PRO-PHAGE', MEANING THAT ITS GENOME IS SILENT INSIDE ITS HOST, E.COLI.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 26% PEG 3350, 50mM TRIS-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	77	1
2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X6A	1	0.92
SYNCHROTRON	CHESS	F1	2	0.92

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2008
Details: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK (RH COATED SI)

Radiation

Monochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK (RH COATED SI)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.92 Å / Relative weight: 1

Reflection

Resolution: 1.1→20 Å / Num. all: 1053320 / Num. obs: 176986 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / R_sym value: 0.072 / Net I/σ(I): 29.96

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.101→9.976 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 15.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.157	2004	1.13 %	RANDOM
R_work	0.1513	-	-	-
obs	0.1514	176682	98.98 %	-
all	-	176682	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.101→9.976 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3466	0	35	754	4255

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3559
X-RAY DIFFRACTION	f_angle_d	1.362	4851
X-RAY DIFFRACTION	f_dihedral_angle_d	11.31	1248
X-RAY DIFFRACTION	f_chiral_restr	0.078	615
X-RAY DIFFRACTION	f_plane_restr	0.007	607

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 (%)
1.1007-1.1281	0.2237	139	0.2131	11496	X-RAY DIFFRACTION	92
1.1281-1.1586	0.1936	135	0.197	12228	X-RAY DIFFRACTION	97
1.1586-1.1926	0.1828	142	0.1802	12300	X-RAY DIFFRACTION	99
1.1926-1.2311	0.1854	141	0.1741	12416	X-RAY DIFFRACTION	99
1.2311-1.275	0.1935	146	0.169	12381	X-RAY DIFFRACTION	99
1.275-1.3259	0.159	140	0.1607	12513	X-RAY DIFFRACTION	99
1.3259-1.3861	0.154	142	0.1567	12494	X-RAY DIFFRACTION	100
1.3861-1.459	0.1553	146	0.1524	12524	X-RAY DIFFRACTION	100
1.459-1.5501	0.1504	144	0.1412	12563	X-RAY DIFFRACTION	100
1.5501-1.6693	0.1556	141	0.14	12605	X-RAY DIFFRACTION	100
1.6693-1.8363	0.1712	146	0.1387	12633	X-RAY DIFFRACTION	100
1.8363-2.0999	0.159	145	0.1321	12675	X-RAY DIFFRACTION	100
2.0999-2.6375	0.1453	146	0.1402	12777	X-RAY DIFFRACTION	100
2.6375-9.9769	0.1397	151	0.1544	13073	X-RAY DIFFRACTION	100

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	1.9696	0.3065	2.0289	0.8453	0.244	3.2959	-0.0101	-0.0094	0.0413	0.0188	0.0017	-0.0028	-0.1575	0.0587	0.0373	0.0704	-0.0012	0.0064	0.0351	-0.0021	0.0507	67.4773	23.4994	21.1647
2	1.3378	0.4355	-0.2027	1.5568	0.6025	1.8386	-0.0894	0.1205	0.1173	-0.1578	0.1152	0.3514	-0.0861	-0.3104	-0.0063	0.1473	-0.0296	-0.0479	0.1539	0.045	0.1329	55.3994	13.7145	-4.4102
3	1.297	-0.8654	0.2123	1.1029	0.0341	1.7711	-0.0479	0.1079	0.1232	-0.0204	0.0015	0.0002	-0.1939	-0.0666	0.0441	0.0927	0.0043	-0.0102	0.0636	0.0197	0.0832	59.9923	23.4404	4.059
4	2.0061	-0.2749	1.607	0.89	-0.2571	2.4328	-0.038	0.1845	0.1246	-0.052	-0.0046	-0.035	-0.1059	0.2238	0.0619	0.0622	-0.0138	0.0101	0.0752	0.0074	0.072	72.1847	20.5926	9.0075
5	0.2209	0.2841	0.1188	0.8255	0.1537	0.5985	-0.0425	-0.0065	0.0138	-0.0863	0.0176	0.0986	0.0092	-0.0465	0.032	0.0491	-0.0013	-0.0105	0.0538	0.0067	0.0626	56.7947	4.9809	3.8416
6	1.2593	-0.4901	0.0274	0.3566	-0.2422	1.1383	-0.0041	0.0602	0.0245	-0.0381	-0.012	-0.0416	-0.0761	0.1502	0.0186	0.0499	-0.0076	0.0028	0.0517	-0.0092	0.057	72.4727	13.3261	9.3464
7	0.6758	0.4937	0.3414	1.0039	0.7299	1.1699	-0.0681	0.0348	0.0412	-0.1147	0.0139	0.108	-0.0793	-0.0734	0.0418	0.0627	0.002	-0.017	0.0485	0.0133	0.0626	57.1769	12.4472	3.5291
8	0.5322	-0.6265	-0.7557	2.6987	2.5498	3.5596	0.0103	0.0077	0.0249	0.1108	0.0372	-0.1183	-0.0284	0.0898	-0.106	0.0379	-0.0098	-0.0094	0.0661	0.0059	0.0663	79.7602	11.4826	25.8716
9	0.2081	0.2557	0.089	0.6492	0.0681	0.9995	-0.0053	0.0404	-0.1122	-0.0696	0.0321	-0.1682	0.1394	0.2282	-0.0377	0.0795	0.0372	0.0127	0.1242	-0.0079	0.1295	80.0192	-8.2998	10.8832
10	1.2141	-0.2003	-0.3941	1.1544	0.429	1.4796	0.0234	-0.0317	-0.0752	0.097	0.0077	-0.0969	0.1193	0.1682	-0.0235	0.0587	0.0171	-0.0179	0.0679	0.0028	0.0688	77.5011	-2.4139	25.9834
11	0.1916	0.2409	0.2376	0.4403	0.2453	0.628	-0.0083	0.0187	-0.0308	-0.0283	0.0429	-0.0228	0.0406	0.0133	-0.0327	0.063	0.0042	0.0016	0.0677	-0.0023	0.065	65.5219	-5.6122	7.8364
12	0.5085	-0.0696	-0.237	0.8393	-0.4738	1.5126	-0.0086	-0.0223	-0.0549	0.0954	0.0195	-0.0538	0.0856	0.0559	-0.0231	0.0495	-0.0023	-0.0121	0.0549	-0.0054	0.058	69.6326	-2.3083	25.624
13	0.4845	0.3339	0.1996	0.9276	0.4631	1.2559	0.0115	0.0394	-0.0588	-0.0249	0.0536	-0.0745	0.0992	0.0566	-0.0702	0.0552	0.0172	-0.001	0.0674	-0.0064	0.0755	72.7435	-5.5225	9.827
14	2.1037	2.291	0.2973	3.3257	0.4429	0.7969	0.0329	-0.0924	0.0203	0.0803	-0.0475	-0.0284	-0.0101	-0.0408	0.022	0.0663	0.0114	-0.0001	0.0582	0.0033	0.0429	64.3012	11.6218	34.293
15	0.7772	0.2824	0.6163	0.7009	0.573	1.0016	0.1245	-0.1159	-0.0721	0.1945	-0.0892	0.145	0.1942	-0.2437	-0.0261	0.1212	-0.0253	0.0276	0.148	0.0197	0.1171	46.9903	-3.4197	28.1764
16	1.1682	0.3832	0.0874	1.3292	-0.029	0.9167	0.019	-0.0979	0.0719	0.1589	-0.0332	0.1878	-0.0105	-0.1818	-0.0016	0.0674	0.0096	0.028	0.0893	-0.0084	0.0806	51.6475	12.3563	29.51
17	0.2012	0.2334	0.2265	0.5746	0.2289	0.636	0.0046	-0.0062	-0.0048	0.0168	0.0072	0.0524	0.0722	-0.0575	-0.0033	0.0545	-0.0056	0.0042	0.0627	0.0079	0.0716	52.9815	-3.6662	14.4636
18	1.217	-1.4855	-0.3567	5.5993	0.3472	0.5509	-0.0188	-0.0412	0.0785	0.0485	0.0492	0.0249	0.0158	-0.0342	-0.0317	0.0537	0.004	-0.0065	0.0562	0.003	0.0383	56.878	11.8041	20.8621
19	0.3863	0.4504	0.4005	1.1789	0.4821	0.7018	0.0437	-0.0313	0.0039	0.0881	-0.0402	0.0995	0.0419	-0.0814	0.0003	0.0502	-0.0016	0.0237	0.0819	0.0068	0.0795	50.2888	2.1955	22.228
20	4.5837	-6.4184	1.5005	9.9367	-4.0757	4.6128	0.006	0.0833	-0.0661	-0.1314	0.1251	-0.1362	0.15	0.0365	-0.1202	0.1031	-0.0136	-0.006	0.0775	-0.0037	0.0986	65.808	-1.9171	29.0421
21	5.31	3.0144	-2.5843	6.2107	-4.4882	5.6285	-0.0119	0.0608	-0.0614	-0.0435	-0.0713	0.0289	-0.1244	-0.054	-0.0221	0.08	-0.0083	0.0005	0.1057	-0.0085	0.0877	76.5889	10.3825	10.5934
22	8.6895	-3.9305	-6.0618	7.1408	2.3027	7.571	0.1141	-0.1599	0.0477	-0.0506	0.0113	0.1192	0.0321	0.0072	-0.1133	0.0653	0.0153	-0.0072	0.0842	-0.0018	0.0914	54.4078	17.4348	18.8847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 166:185 )	A	166 - 185
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 186:197 )	A	186 - 197
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 198:217 )	A	198 - 217
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 218:231 )	A	218 - 231
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 232:275 )	A	232 - 275
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 276:296 )	A	276 - 296
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 297:317 )	A	297 - 317
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 164:185 )	B	164 - 185
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 186:214 )	B	186 - 214
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 215:231 )	B	215 - 231
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 232:275 )	B	232 - 275
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 276:296 )	B	276 - 296
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 297:317 )	B	297 - 317
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 166:185 )	C	166 - 185
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 186:214 )	C	186 - 214
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 215:231 )	C	215 - 231
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 232:275 )	C	232 - 275
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 276:288 )	C	276 - 288
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 289:317 )	C	289 - 317
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 401:401 )	C	401
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 401:401 )	B	401
22	X-RAY DIFFRACTION	22	( CHAIN A AND RESID 401:401 )	A	401

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