PDB-2vky: Headbinding Domain of Phage P22 Tailspike C-Terminally Fused to I...

ID or keywords:

Entry

Database: PDB / ID: 2vky

Title

Headbinding Domain of Phage P22 Tailspike C-Terminally Fused to Isoleucine Zipper pIIGCN4 (Chimera I)

Components

TAIL PROTEIN, PIIGCN4

Keywords

VIRAL PROTEIN / HEAD-BINDING DOMAIN / PHAGE P22 TAILSPIKE / CHIMERA / HYDROLASE / LATE PROTEIN / ISOLEUCINE ZIPPER PIIGCN4

Function / homology

Function and homology information

endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell
Similarity search - Function

Biological species

ENTEROBACTERIA PHAGE P22 (virus)

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seul, A. / Mueller, J.J. / Mueller, G. / Heinemann, U. / Seckler, R.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Bacteriophage P22 Tailspike: Structure of the Complete Protein and Function of the Interdomain Linker
Authors: Seul, A. / Mueller, J.J. / Andres, D. / Stettner, E. / Heinemann, U. / Seckler, R.

History

Deposition	Jan 4, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	May 14, 2014	Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2	May 21, 2014	Group: Database references
Revision 1.3	Mar 15, 2017	Group: Source and taxonomy
Revision 1.4	Jun 13, 2018	Group: Data collection / Database references / Structure summary Category: citation / struct / Item: _citation.page_last / _struct.title
Revision 1.5	Jan 30, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2vky.cif.gz	79.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2vky.ent.gz	60.4 KB	Display	PDB format
PDBx/mmJSON format	2vky.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2vky_validation.pdf.gz	422.2 KB	Display	wwPDB validaton report
Full document	2vky_full_validation.pdf.gz	422.3 KB	Display
Data in XML	2vky_validation.xml.gz	9.7 KB	Display
Data in CIF	2vky_validation.cif.gz	13.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/2vky ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vky	HTTPS FTP

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Related structure data

Related structure data	2vnlC 2xc1C 1eboS 1lktS 1clw 1qa1 1qa2 1qa3 1qq1 1qrb 1qrc 1tsp 1tyv 2vfm 2vfn 2vfo 2vfp 2vfq S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fhw-2 4pk1-d 4kqq-2 6bkq-2 6feg-d 2r32-1 3rac-1 6tix-1 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

B: TAIL PROTEIN, PIIGCN4

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

1

B: TAIL PROTEIN, PIIGCN4

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

Unit cell

Length a, b, c (Å)	57.810, 57.810, 107.120
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	B-2009- HOH
2	1	B-2015- HOH

#1: Protein	TAIL PROTEIN, PIIGCN4 / TAILSPIKE-PROTEIN Mass: 17216.551 Da / Num. of mol.: 1 / Fragment: HEAD-BINDING DOMAIN, RESIDUES 2-124 / Mutation: YES Source method: isolated from a genetically manipulated source Details: AMINO ACIDS 2-124 OF PHAGE P22 TAILSPIKE HAVE BEEN LINKED TO THE ISOLEUCINE ZIPPER PIIGCN4 125-155 Source: (gene. exp.) ENTEROBACTERIA PHAGE P22 (virus), (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: SALMONELLA ENTERICA TYPHIMURIUM / Description: PIIGCN4, MODIFIED SEQUENCE NCBI GI\:5542583 / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12528
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN B, TYR 124 TO LEU
Sequence details	RESIDUES 125 TO 155 ARE NOT FOUND IN UNIPROT ENTRY P12528 BUT ARE PART OF GENBANK ENTRY GI:5542583. ...RESIDUES 125 TO 155 ARE NOT FOUND IN UNIPROT ENTRY P12528 BUT ARE PART OF GENBANK ENTRY GI:5542583. M1 OF GI5542583 IS MUTATED TO I125 IN THIS ENTRY.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 59 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 6.5 Details: VAPOR DIFFUSION, HANGING DROP. PROTEIN: CONC. 8.2 MG/ML,BUFFER 50MM HEPES, PH6.5; RESERVOIR: 20% ISOPROPANOL, 0.1M NA-ACETATE, PH4.6, 0.2M CACL2; DROPLET 2 MICROL: 2 MICROL.CRYO:30% GLYCEROL.

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU H2B / Wavelength: 1.5418
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 8, 2005 / Details: SLITS
Radiation	Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.05→19.7 Å / Num. obs: 12716 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / B_iso Wilson estimate: 30.86 Å² / R_sym value: 0.03 / Net I/σ(I): 31.66
Reflection shell	Resolution: 2.05→2.2 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 13.6 / R_sym value: 0.1 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1LKT, 1EBO

1lkt

1ebo

Resolution: 2.05→20 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.941 / SU B: 5.75 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE HEAD-BINDING DOMAIN IS FUSED TO THE ISOLEUCINE ZIPPER PIIGCN4. THE BIOLOGICALLY ACTIVE HEAD- BINDING DOMAIN IS A CRYSTALLOGRAPHIC TRIMER.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.187	622	4.9 %	RANDOM
R_work	0.145	-	-	-
obs	0.147	12111	99.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 24.46 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.73 Å²	-0.37 Å²	0 Å²
2-	-	-0.73 Å²	0 Å²
3-	-	-	1.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1197	0	0	173	1370

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	1217
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1118
X-RAY DIFFRACTION	r_angle_refined_deg	1.45	1.96	1651
X-RAY DIFFRACTION	r_angle_other_deg	0.771	3	2623
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.599	5	151
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.184	26.429	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.98	15	221
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	4.875	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	192
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1338
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	209
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	241
X-RAY DIFFRACTION	r_nbd_other	0.168	0.2	1100
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	613
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	690
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	92
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.166	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.218	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.192	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.511	2	996
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.846	3	1241
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	5.756	4.5	534
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	7.579	6	410
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.05→2.16 Å / Total num. of bins used: 10 /

	R_factor	Num. reflection
R_free	0.199	93
R_work	0.134	1748

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	4.5121	-0.704	-3.0819	0.8208	1.4503	4.5907	0.2178	-0.5033	0.3111	0.0372	0.0771	-0.099	-0.1495	0.3846	-0.2949	0.0607	-0.0353	-0.014	0.0418	-0.0026	0.0438	1.5679	35.4362	-3.6945
2	2.7015	-0.4497	-0.1913	26.8096	-1.4893	1.5429	0.0803	0.1751	0.1025	0.2	-0.1465	0.4361	0.0027	0.166	0.0662	0.0221	-0.0268	-0.0154	0.0575	-0.0453	-0.0248	4.29	29.8403	-20.5545
3	10.2184	0.2743	8.2532	5.4584	1.4552	12.9721	-0.1255	0.112	-0.1585	-0.0922	0.088	0.0809	-0.0568	-0.0246	0.0375	-0.057	0.0081	-0.0047	-0.0693	0.0022	0.0231	10.2682	19.0208	-8.4557
4	9.2951	0.1039	2.427	5.9075	-3.0858	2.2745	-0.0465	-0.2708	-0.1442	-0.0122	-0.1523	0.0468	-0.1974	-0.3875	0.1988	-0.0262	0.0195	-0.0171	-0.0227	0.0047	0.0179	16.4185	16.1914	-4.374
5	12.3841	-0.2404	0.4243	2.1638	-0.8404	0.3353	-0.0885	-0.9369	0.137	0.1815	0.0559	0.1422	0.0301	-0.0214	0.0326	0.0051	0.0146	-0.0038	0.0995	-0.014	0.0429	8.3282	15.2743	-0.5897
6	9.7512	-0.9036	-4.441	1.1434	-0.0086	5.908	0.0083	-0.2391	-0.2311	-0.045	-0.0786	0.1329	0.1504	0.4164	0.0703	0.0331	0.025	-0.0501	0.0299	-0.0203	0.0149	8.3813	13.5936	-8.8904
7	5.7806	-0.2519	0.6559	7.0094	-5.0202	3.6347	0.0899	0.0631	-0.1408	-0.2508	0.3246	0.3759	0.0777	-0.0214	-0.4144	0.0359	-0.0078	-0.0289	0.0117	-0.0209	0.0036	-3.4069	22.1467	-16.9932
8	6.7645	0.382	7.2169	3.0731	2.1605	15.6461	-0.2221	-0.1821	-0.0125	-0.2829	-0.0786	0.4249	-0.4639	-0.8085	0.3007	0.0448	-0.0034	-0.0408	0.059	0.0028	0.0808	-5.5847	18.9682	-9.1448
9	3.1295	-0.6847	2.1418	1.7019	-0.7385	15.3672	-0.0197	-0.1013	-0.0679	-0.0143	0.0722	-0.0298	-0.2756	-0.3283	-0.0525	-0.0058	0.0031	-0.012	-0.0194	-0.0258	0.0314	10.0683	21.6473	-5.9352
10	3.9895	0.8487	2.7314	1.6632	-1.2981	11.0473	-0.1376	0.0858	0.0242	0.0088	-0.067	0.0974	-0.3864	0.6941	0.2046	0.0306	-0.0174	0.0058	0.001	-0.0094	0.0316	14.9929	25.6177	-5.715
11	44.5819	0.566	-4.5487	3.0398	2.8583	3.7992	0.1902	0.4911	0.6236	-0.0118	-0.2091	0.2923	-0.1544	-0.1833	0.0189	0.0842	0.0661	-0.0026	-0.0182	0.0246	0.0578	2.6232	26.395	-0.4932
12	8.7847	0.0863	-7.2908	5.2816	13.6275	41.5889	0.1604	0.0096	-0.0529	-0.4706	-0.2139	0.0546	-0.7707	-0.0882	0.0535	0.081	0.037	-0.0135	0.1092	0.0018	0.0897	-6.7523	27.6816	6.7875
13	9.3803	-1.2471	-6.1271	13.3562	16.1769	72.3209	-0.2219	-0.3226	0.0546	0.1759	-0.1945	0.0812	0.0658	-0.2989	0.4164	0.0876	0.0172	-0.0454	0.156	-0.0464	0.0702	-6.6422	28.2481	17.7353
14	11.8212	-1.3076	7.3715	9.6182	14.0964	44.0491	0.0162	0.8716	-0.3776	-0.8173	-0.0179	0.0396	-1.6058	0.741	0.0017	0.1778	-0.0599	-0.0245	0.1842	-0.0206	0.029	-5.3383	32.0932	25.321
15	14.6884	2.917	-4.5896	9.1362	11.1138	57.7191	-0.0541	0.1466	-0.6388	-0.3425	-0.0362	-0.0327	0.0084	-0.7446	0.0903	0.0458	-0.0301	-0.0195	0.0349	-0.0231	0.0338	-6.3342	30.5818	33.2769
16	4.8048	-0.3521	2.5853	2.1753	1.0858	13.4915	0.1571	0.3418	-0.4921	0.0436	0.0735	0.2219	1.3686	1.1273	-0.2306	0.1128	0.1037	0.017	0.0132	-0.0131	0.0068	0.8388	27.4969	46.2437
17	6.5796	-1.3944	3.981	5.3639	0.3788	26.343	-0.0925	-0.1916	0.1091	0.2604	-0.0362	0.2313	-0.0439	0.2422	0.1287	-0.0326	0.0179	0.0123	-0.0524	0.013	0.0244	-5.5071	36.0489	50.6177

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	3 - 21
2	X-RAY DIFFRACTION	2	B	22 - 29
3	X-RAY DIFFRACTION	3	B	30 - 36
4	X-RAY DIFFRACTION	4	B	37 - 42
5	X-RAY DIFFRACTION	5	B	43 - 50
6	X-RAY DIFFRACTION	6	B	51 - 65
7	X-RAY DIFFRACTION	7	B	66 - 74
8	X-RAY DIFFRACTION	8	B	75 - 86
9	X-RAY DIFFRACTION	9	B	87 - 95
10	X-RAY DIFFRACTION	10	B	96 - 105
11	X-RAY DIFFRACTION	11	B	106 - 110
12	X-RAY DIFFRACTION	12	B	111 - 115
13	X-RAY DIFFRACTION	13	B	116 - 123
14	X-RAY DIFFRACTION	14	B	124 - 128
15	X-RAY DIFFRACTION	15	B	129 - 133
16	X-RAY DIFFRACTION	16	B	134 - 141
17	X-RAY DIFFRACTION	17	B	142 - 154

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