PDB-2vji: Tailspike protein of E.coli bacteriophage HK620

ID or keywords:

Entry

Database: PDB / ID: 2vji

Title

Tailspike protein of E.coli bacteriophage HK620

Components

TAILSPIKE PROTEIN

Keywords

VIRAL PROTEIN / VIRAL ADHESION PROTEIN / ENDO-N-ACETYLGLUCOSAMINIDASE / RIGHT-HANDED PARALLEL BETA-HELIX / HYDROLASE / TAILSPIKE

Function / homology

Function and homology information

biological process involved in interaction with host / viral life cycle / virion component / metal ion binding
Similarity search - Function

Biological species

BACTERIOPHAGE HK620 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.38 Å

Authors

Mueller, J.J. / Barbirz, S. / Uetrecht, C. / Seckler, R. / Heinemann, U.

Citation

Journal: Mol.Microbiol. / Year: 2008
Title: Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related.
Authors: Barbirz, S. / Mueller, J.J. / Uetrecht, C. / Clark, A.J. / Heinemann, U. / Seckler, R.

History

Deposition	Dec 11, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2012	Group: Advisory / Other / Version format compliance
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vji.cif.gz	263.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2vji.ent.gz	213.2 KB	Display	PDB format
PDBx/mmJSON format	2vji.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2vji_validation.pdf.gz	453 KB	Display	wwPDB validaton report
Full document	2vji_full_validation.pdf.gz	455.4 KB	Display
Data in XML	2vji_validation.xml.gz	32.4 KB	Display
Data in CIF	2vji_validation.cif.gz	52.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vj/2vji ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vji	HTTPS FTP

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Related structure data

Related structure data	2vjjC C: citing same article (ref.)
Similar structure data	4xle-1 6gvr-1 4xl9-1 4xnf-1 4yel-1 4xop-1 4xlc-1 2x85-1 2vjj-1 4xkv-1 4xon-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

A: TAILSPIKE PROTEIN

hetero molecules

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

1

A: TAILSPIKE PROTEIN

hetero molecules

A: TAILSPIKE PROTEIN

hetero molecules

A: TAILSPIKE PROTEIN

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.216, 74.216, 175.160
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-2059- HOH
2	1	A-2130- HOH
3	1	A-2193- HOH
4	1	A-2361- HOH
5	1	A-2481- HOH
6	1	A-2523- HOH
7	1	A-2526- HOH
8	1	A-2528- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	TAILSPIKE PROTEIN / HK620 TAILSPIKE PROTEIN Mass: 64705.355 Da / Num. of mol.: 1 Fragment: LACKING THE N-TERMINAL HEAD-BINDING DOMAIN, RESIDUES 111-710 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTERIOPHAGE HK620 (virus) / Strain: H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9AYY6

#1: Protein

TAILSPIKE PROTEIN / HK620 TAILSPIKE PROTEIN

Mass: 64705.355 Da / Num. of mol.: 1
Fragment: LACKING THE N-TERMINAL HEAD-BINDING DOMAIN, RESIDUES 111-710
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

BACTERIOPHAGE HK620 (virus) / Strain: H / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9AYY6

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Non-polymers , 5 types, 939 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₂O₃ / Comment: inhibitor, precipitant*YM
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	THE SEQUENCE WAS NUMBERED WITHOUT THE N-TERMINAL MET FROM 1 TO 709 (SWISSPROT 1 TO 710)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 3 Details: VAPOR DIFFUSION,HANGING DROP: PROTEIN CONCENTRATION 3MG/ML,5% PEG1500,PH3.0. RESERVOIR: 10% PEG 1500, PH 3.0. DROPLET 3 MICRO LITER: 3 MICRO LITER. CRYO CONDITION:30% PEG1500.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 8, 2001 / Details: TOROIDAL ZERODUR MIRROR
Radiation	Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.38→20 Å / Num. obs: 115675 / % possible obs: 97.5 % / Redundancy: 4.6 % / B_iso Wilson estimate: 14.6 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.38→1.43 Å / Redundancy: 4 % / R_merge(I) obs: 0.26 / Mean I/σ(I) obs: 5.1 / % possible all: 90.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data reduction
XSCALE		data scaling
SOLVE	RESOLVE V2.09	phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.38→20 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.964 / SU B: 2.023 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18	5722	5 %	RANDOM
R_work	0.15	-	-	-
obs	0.151	108474	98.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 11.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.71 Å²	0.35 Å²	0 Å²
2-	-	0.71 Å²	0 Å²
3-	-	-	-1.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.38→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4536	0	17	935	5488

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	4806
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4129
X-RAY DIFFRACTION	r_angle_refined_deg	1.499	1.919	6567
X-RAY DIFFRACTION	r_angle_other_deg	0.813	3	9572
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.767	5	623
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.59	24.217	230
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.089	15	700
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.324	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	724
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5607
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1044
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	1005
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	4418
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2491
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	2818
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	722
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	0.146	0.2	44
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.197	0.2	161
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.169	0.2	149
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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: 1.38→1.43 Å / Total num. of bins used: 15

	R_factor	Num. reflection	% reflection
R_free	0.237	496	-
R_work	0.208	9521	-
obs	-	-	89.37 %

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	7.8294	4.9389	-1.5302	10.5718	1.0672	23.2109	-0.2218	0.5774	0.0993	-0.8271	0.3821	-0.2027	-0.1052	-0.1073	-0.1603	0.1624	-0.0346	0.0058	0.1165	0.0328	-0.0481	-33.0643	-15.226	-18.3785
2	3.2145	1.0893	-0.4619	0.7246	0.393	0.9161	0.0074	0.0315	0.014	-0.0988	-0.0456	0.0321	-0.0869	-0.2248	0.0382	0.1003	0.0013	-0.0184	0.1398	0.0001	-0.0343	-45.1227	-19.1288	-4.7306
3	0.748	0.4996	0.0405	0.4524	-0.5868	3.177	-0.1152	0.0905	-0.0171	-0.2126	-0.0778	0.0309	-0.034	0.4167	0.193	0.1134	-0.049	0.0202	0.1313	0.0523	-0.0718	-22.6963	-11.1799	5.2281
4	2.1373	-0.02	-0.0234	0.4253	-1.0181	2.4395	-0.0173	0.1112	0.297	-0.1029	-0.2296	-0.0025	-0.4414	0.3042	0.2469	0.1528	-0.0805	-0.0142	0.095	0.0792	-0.0388	-22.9331	-3.2706	15.4994
5	13.5123	7.5586	2.9766	7.2946	2.1314	3.1114	-0.0489	0.385	-0.1978	-0.2573	-0.0232	-0.1239	0.088	0.5143	0.072	0.0799	-0.0104	0.08	0.2465	0.0983	-0.0945	-14.7459	-15.0857	14.47
6	7.4964	-0.7314	4.2748	1.8132	0.2366	5.5739	-0.1121	0.4544	0.2488	-0.2621	-0.0973	-0.0578	-0.3305	0.6391	0.2094	0.0577	-0.1333	0.0414	0.2219	0.1312	-0.0143	-10.3983	-5.9698	20.1399
7	4.1369	-0.6415	-1.8146	2.5267	2.0128	3.1691	0.2504	0.0507	0.6065	-0.341	-0.0507	-0.1146	-0.6837	0.1787	-0.1997	0.2374	-0.0538	0.0069	0.0437	0.0711	0.0222	-26.9419	3.6114	21.1326
8	0.7123	-0.1726	-0.0343	0.6595	-0.0637	1.1642	-0.0258	0.1065	0.0661	-0.122	-0.0627	-0.0688	-0.1345	0.2697	0.0884	0.0747	-0.0399	0.0055	0.102	0.0544	0.0122	-21.4182	-9.7794	26.8171
9	6.8481	-9.3779	-1.2655	17.2267	2.8477	3.329	-0.1327	0.0213	-0.2049	-0.0931	0.0335	0.4036	-0.0417	-0.0356	0.0992	0.0652	-0.0077	-0.0136	0.0544	0.0276	0.0248	-34.3908	-8.9887	33.9056
10	0.4758	-0.1905	0.07	0.4571	-0.0154	0.9384	-0.0514	0.0481	0.0745	-0.0292	-0.0223	-0.0359	-0.1395	0.1338	0.0738	0.048	-0.0186	-0.0076	0.0464	0.0334	0.0321	-24.5529	-10.1036	41.5135
11	3.3125	0.5741	-0.4626	7.7623	0.088	1.1724	0.0951	0.1924	-0.0497	-0.1092	-0.1139	-0.0717	0.0278	0.3693	0.0188	0.0025	0.0084	0.0193	0.156	0.0247	0.0652	-7.8542	-19.3582	49.3135
12	1.0159	-0.4004	0.0711	1.0152	0.1467	0.8825	-0.0065	0.0649	0.1552	-0.069	-0.0284	-0.1081	-0.1016	0.1012	0.0349	0.0591	-0.0144	0.0074	0.0588	0.0279	0.074	-22.2267	-10.6059	53.2857
13	0.8349	-0.3797	-0.1943	1.3819	0.1251	0.6904	0.0025	-0.0061	0.0686	-0.0074	-0.0197	-0.1257	-0.0152	0.0973	0.0172	0.058	-0.0075	-0.0013	0.0694	0.0119	0.089	-21.4772	-14.5171	60.4185
14	0.1783	-0.1719	-0.1189	0.7968	0.0685	0.3196	-0.0008	-0.0097	0.0162	-0.0046	-0.0084	-0.0872	-0.0143	0.0959	0.0091	0.0223	-0.0019	0.0002	0.0352	0.0074	0.0953	-19.2716	-15.944	67.2036
15	4.9631	-1.576	1.6373	0.5342	-0.4444	0.7089	-0.188	0.0944	0.4392	0.0776	0.0303	-0.1922	-0.1972	0.118	0.1578	0.0422	-0.0387	-0.0183	0.0245	0.0112	0.1341	-20.9053	-1.684	70.9798
16	0.3085	-0.0518	-0.0406	0.2312	0.059	0.1456	-0.0011	-0.0282	0.0249	0.0138	0.0062	-0.0838	-0.0442	0.0646	-0.005	0.0256	0.0063	0.0002	0.0178	-0.0007	0.0824	-24.0691	-14.7942	76.3487
17	3.69	1.6882	-1.592	4.3623	-3.067	3.2324	0.1034	-0.0841	0.1865	0.0856	-0.0258	0.2092	0.0063	0.0374	-0.0776	0.0115	0.0237	0.002	0.0306	-0.0109	0.0995	-26.6216	-22.008	102.1506
18	0.8567	-0.4338	0.9149	1.0909	-0.2321	1.0384	-0.0347	0.0218	0.0592	-0.0238	-0.024	-0.1587	-0.0315	0.1222	0.0587	0.008	0.0091	0.0158	0.0358	0.003	0.1126	-25.0632	-17.3957	88.3414
19	1.1357	-0.3062	0.4341	0.2734	-0.5808	1.2926	0.0295	-0.0691	-0.0322	-0.066	0.0519	0.0719	0.1169	0.0712	-0.0815	0.0472	0.0168	-0.0072	0.0289	-0.0067	0.1225	-28.6363	-21.3094	94.7664
20	0.4504	-0.2328	0.2585	0.1662	0.0351	0.7686	0.0241	-0.0129	-0.0441	-0.0075	0.0247	0.0357	0.0298	0.0327	-0.0488	0.0384	0.007	-0.0024	0.0473	0.0027	0.1184	-26.7182	-22.0574	90.507

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	112 - 122
2	X-RAY DIFFRACTION	2	A	123 - 149
3	X-RAY DIFFRACTION	3	A	150 - 202
4	X-RAY DIFFRACTION	4	A	203 - 226
5	X-RAY DIFFRACTION	5	A	227 - 235
6	X-RAY DIFFRACTION	6	A	236 - 243
7	X-RAY DIFFRACTION	7	A	244 - 259
8	X-RAY DIFFRACTION	8	A	260 - 347
9	X-RAY DIFFRACTION	9	A	348 - 353
10	X-RAY DIFFRACTION	10	A	354 - 452
11	X-RAY DIFFRACTION	11	A	453 - 460
12	X-RAY DIFFRACTION	12	A	461 - 516
13	X-RAY DIFFRACTION	13	A	517 - 550
14	X-RAY DIFFRACTION	14	A	551 - 590
15	X-RAY DIFFRACTION	15	A	591 - 596
16	X-RAY DIFFRACTION	16	A	597 - 635
17	X-RAY DIFFRACTION	17	A	636 - 647
18	X-RAY DIFFRACTION	18	A	648 - 666
19	X-RAY DIFFRACTION	19	A	667 - 690
20	X-RAY DIFFRACTION	20	A	691 - 709

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Protein , 1 types, 1 molecules A

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Non-polymers , 5 types, 939 molecules

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Protein , 1 types, 1 molecules A

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Non-polymers , 5 types, 939 molecules

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