PDB-5bvz: HK620 Tail Needle crystallized at pH 9 (Crystal form II)

ID or keywords:

Entry

Database: PDB / ID: 5bvz

Title

HK620 Tail Needle crystallized at pH 9 (Crystal form II)

Components

DNA stabilization protein

Keywords

VIRAL PROTEIN / tail needle / viral genome-ejection / Coiled coil / trimer / bacteriophage

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Enterobacteria phage HK620 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Bhardwaj, A. / Cingolani, G.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM100888	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	P30 CA56036	United States

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions.
Authors: Bhardwaj, A. / Sankhala, R.S. / Olia, A.S. / Brooke, D. / Casjens, S.R. / Taylor, D.J. / Prevelige, P.E. / Cingolani, G.

History

Deposition	Jun 5, 2015	Deposition site: RCSB / Processing site: RCSB
Supersession	Jun 24, 2015	ID: 4FOH
Revision 1.0	Jun 24, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 25, 2015	Group: Data collection / Database references
Revision 1.2	Dec 2, 2015	Group: Database references
Revision 1.3	Jan 13, 2016	Group: Database references
Revision 1.4	Sep 13, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	5bvz.cif.gz	424 KB	Display	PDBx/mmCIF format
PDB format	pdb5bvz.ent.gz	348.1 KB	Display	PDB format
PDBx/mmJSON format	5bvz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5bvz_validation.pdf.gz	477.2 KB	Display	wwPDB validaton report
Full document	5bvz_full_validation.pdf.gz	485.5 KB	Display
Data in XML	5bvz_validation.xml.gz	40.6 KB	Display
Data in CIF	5bvz_validation.cif.gz	57 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bv/5bvz ftp://data.pdbj.org/pub/pdb/validation_reports/bv/5bvz	HTTPS FTP

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Related structure data

Related structure data	4zkpC 4zkuC 4zxqC 5bu5C 5bu8C 3c9iS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zkp-2 4zku-1 4zku-2 4zkp-1 5bu8-2 6pgw-d 5bu5-2 5bu5-1 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: DNA stabilization protein

B: DNA stabilization protein

C: DNA stabilization protein

D: DNA stabilization protein

E: DNA stabilization protein

F: DNA stabilization protein

hetero molecules

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

1

A: DNA stabilization protein

B: DNA stabilization protein

C: DNA stabilization protein

hetero molecules

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

2

D: DNA stabilization protein

E: DNA stabilization protein

F: DNA stabilization protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.002, 73.812, 77.633
Angle α, β, γ (deg.)	83.21, 66.41, 70.66
Int Tables number	1
Space group name H-M	P1

#1: Protein	DNA stabilization protein / Phage HK620 tail needle gp26 Mass: 25084.785 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage HK620 (virus) / Gene: 26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9AYZ3
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.88 Å³/Da / Density % sol: 34.45 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 40% PEG 4000, 0.1M potassium chloride, 0.1M TAPS buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2007
Radiation	Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9179 Å / Relative weight: 1
Reflection	Resolution: 2.5→15 Å / Num. all: 71365 / Num. obs: 37023 / % possible obs: 98.1 % / Redundancy: 1.9 % / R_sym value: 0.114 / Net I/σ(I): 9.04
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.327 / R_sym value: 0.4 / % possible all: 95

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data collection
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3C9I

3c9i

Resolution: 2.5→15 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2597	1763	5.16 %	Random selection
R_work	0.209	-	-	-
obs	0.2116	37023	89.04 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8178	0	4	347	8529

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8256
X-RAY DIFFRACTION	f_angle_d	0.787	11250
X-RAY DIFFRACTION	f_dihedral_angle_d	11.682	2964
X-RAY DIFFRACTION	f_chiral_restr	0.031	1404
X-RAY DIFFRACTION	f_plane_restr	0.004	1464

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 (%)
2.4947-2.5287	0.3277	93	0.2935	1883	X-RAY DIFFRACTION	66
2.5287-2.5647	0.3863	154	0.2872	2383	X-RAY DIFFRACTION	84
2.5647-2.6028	0.3772	132	0.2844	2508	X-RAY DIFFRACTION	88
2.6028-2.6432	0.359	137	0.2856	2551	X-RAY DIFFRACTION	88
2.6432-2.6863	0.3654	127	0.2863	2531	X-RAY DIFFRACTION	88
2.6863-2.7324	0.2949	139	0.2813	2545	X-RAY DIFFRACTION	88
2.7324-2.7817	0.3059	156	0.2599	2463	X-RAY DIFFRACTION	89
2.7817-2.8349	0.343	125	0.245	2658	X-RAY DIFFRACTION	89
2.8349-2.8924	0.3246	142	0.2501	2510	X-RAY DIFFRACTION	89
2.8924-2.9548	0.311	155	0.2442	2585	X-RAY DIFFRACTION	89
2.9548-3.023	0.2759	132	0.2492	2551	X-RAY DIFFRACTION	90
3.023-3.0979	0.2998	129	0.2263	2561	X-RAY DIFFRACTION	89
3.0979-3.1809	0.2764	145	0.2331	2618	X-RAY DIFFRACTION	90
3.1809-3.2736	0.3281	132	0.2221	2583	X-RAY DIFFRACTION	91
3.2736-3.3781	0.2679	151	0.1991	2645	X-RAY DIFFRACTION	91
3.3781-3.4974	0.2506	148	0.1859	2619	X-RAY DIFFRACTION	91
3.4974-3.6355	0.204	168	0.1807	2569	X-RAY DIFFRACTION	91
3.6355-3.7984	0.2018	136	0.1875	2667	X-RAY DIFFRACTION	91
3.7984-3.9951	0.2142	135	0.1677	2615	X-RAY DIFFRACTION	91
3.9951-4.2401	0.2334	140	0.1585	2634	X-RAY DIFFRACTION	92
4.2401-4.5589	0.209	130	0.1606	2658	X-RAY DIFFRACTION	92
4.5589-5.0022	0.2526	151	0.1847	2625	X-RAY DIFFRACTION	92
5.0022-5.6912	0.2239	114	0.2016	2725	X-RAY DIFFRACTION	93
5.6912-7.0447	0.2483	153	0.222	2681	X-RAY DIFFRACTION	93
7.0447-15.0079	0.1877	161	0.1735	2635	X-RAY DIFFRACTION	93

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	2.0898	-3.4004	3.0361	6.0433	-4.669	4.3852	-0.3464	0.0704	0.3301	0.5015	-0.1179	-0.4956	-0.4452	0.1345	0.4393	0.1871	-0.0399	0.0283	0.2448	0.0401	0.2866	-46.6222	82.5511	-56.1837
2	2.0546	-1.4856	1.7796	2.6596	-2.0066	2.6567	0.0044	-0.0156	0.068	0.0308	-0.0416	-0.0638	-0.023	0.0853	0.0517	0.1562	-0.014	0.0294	0.1652	-0.0219	0.1522	-11.1439	17.99	8.3906
3	1.2419	-1.7183	2.404	4.4222	-5.2663	6.6718	-0.2039	-0.1143	0.0244	0.4238	0.4176	0.1286	-0.4223	-0.4652	-0.3192	0.2953	0.0325	0.0806	0.2196	-0.0763	0.2213	-46.7928	81.3255	-57.3141
4	0.6499	-0.2811	0.7438	1.3606	-0.8702	1.9426	0.039	0.0105	0.0392	0.0573	0.0327	-0.0284	0.0435	-0.0113	-0.0302	0.2373	0.0152	0.0265	0.231	-0.0321	0.2455	-14.7546	18.1421	10.4741
5	0.3949	-1.2735	1.0296	4.0009	-3.0957	3.0519	0.0127	-0.0445	-0.0235	-0.2576	0.0375	0.0428	0.1294	-0.0292	-0.0335	0.1051	-0.0477	-0.0361	0.2638	-0.003	0.3253	-43.83	77.1874	-51.7198
6	0.9244	-0.7305	0.8574	1.7692	-1.1431	1.9696	-0.0308	-0.0058	0.0137	-0.0028	-0.0216	-0.1244	0.1115	-0.0061	0.0462	0.231	-0.0118	0.0222	0.1709	-0.0611	0.201	-12.0587	12.4494	9.4391
7	0.9105	-1.964	1.9773	6.0987	-5.4126	5.9645	0.0953	0.0302	0.0598	-0.3344	-0.1234	-0.0648	0.4879	0.1074	0.0349	0.0897	0.0457	0.0208	0.2635	-0.0573	0.2781	-14.3454	48.4643	13.4146
8	0.8136	-0.3845	1.02	1.3285	-1.3454	2.3429	0.1216	-0.0781	-0.1297	-0.0048	0.0727	0.1885	0.0793	-0.1489	-0.1508	0.1935	-0.0254	0.0056	0.2055	-0.0007	0.2344	-43.338	113.3056	-53.8347
9	1.7215	-1.6742	2.2705	2.1751	-2.5668	3.8615	-0.0241	-0.0732	-0.0476	0.0548	0.0649	0.0707	-0.0087	-0.0166	-0.1243	0.1882	-0.0365	-0.009	0.2129	-0.0409	0.302	-13.9197	49.4457	14.4278
10	0.6697	-0.3073	0.7242	1.7378	-1.0679	1.6547	0.1418	-0.0675	-0.216	-0.0816	0.099	0.1375	0.0626	-0.06	-0.2718	0.2361	-0.0551	-0.0362	0.2065	-0.0048	0.2831	-47.3172	112.614	-52.8293
11	1.2322	-2.4294	1.8133	7.63	-4.4653	3.4656	-0.0517	-0.0674	0.0739	0.1318	0.1051	-0.1042	0.0475	-0.1574	0.0651	0.1939	-0.0436	0.0305	0.2126	-0.04	0.203	-13.1007	49.1927	13.1806
12	0.6499	-0.7278	1.2295	2.1517	-1.8489	2.3583	0.0055	-0.1336	-0.1305	0.0918	0.072	-0.0856	-0.0288	-0.2352	-0.0305	0.2352	-0.0313	-0.0254	0.2263	-0.0218	0.2721	-45.2455	115.7106	-50.9115

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 54 through 139 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 140 through 233 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 54 through 139 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 140 through 233 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 54 through 149 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 150 through 233 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 54 through 139 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 140 through 233 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 54 through 139 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 140 through 233 )
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 54 through 139 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 140 through 233 )

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