PDB-4uw8: Structure of the carboxy-terminal domain of the bacteriophage T5 ...

Basic information

• Entry: Database: PDB / ID: 4uw8
• Title: Structure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail fiber with its intra-molecular chaperone domain
• Components: L-SHAPED TAIL FIBER PROTEIN
• Keywords: VIRAL PROTEIN / BACTERIAL VIRUSES / CAUDOVIRALES / SIPHOVIRIDAE / INFECTION

Function / homology

Function:

lipopolysaccharide-mediated virion attachment to host cell / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / symbiont entry into host cell / proteolysis

Domain/homology:

Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Winged helix-like DNA-binding domain superfamily

Component:

CITRATE ANION / Side tail fiber protein pb1

• Biological species: ENTEROBACTERIA PHAGE T5 (virus)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
• Authors: Garcia-Doval, C. / Luque, D. / Caston, J.R. / Otero, J.M. / Llamas-Saiz, A.L. / Boulanger, P. / van Raaij, M.J.

Citation

Journal: Viruses / Year: 2015
Title: Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.
Authors: Garcia-Doval, C. / Caston, J.R. / Luque, D. / Granell, M. / Otero, J.M. / Llamas-Saiz, A.L. / Renouard, M. / Boulanger, P. / van Raaij, M.J.

#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization of the C-Terminal Domain of the Bacteriophage T5 L-Shaped Fibre.
Authors: Garcia-Doval, C. / Luque, D. / Caston, J.R. / Boulanger, P. / van Raaij, M.J.

History

Deposition	Aug 8, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 16, 2015	Group: Database references / Structure summary
Revision 1.2	Dec 30, 2015	Group: Database references
Revision 1.3	Jan 17, 2018	Group: Database references / Category: citation / citation_author Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: L-SHAPED TAIL FIBER PROTEIN

B: L-SHAPED TAIL FIBER PROTEIN

C: L-SHAPED TAIL FIBER PROTEIN

D: L-SHAPED TAIL FIBER PROTEIN

E: L-SHAPED TAIL FIBER PROTEIN

F: L-SHAPED TAIL FIBER PROTEIN

G: L-SHAPED TAIL FIBER PROTEIN

H: L-SHAPED TAIL FIBER PROTEIN

I: L-SHAPED TAIL FIBER PROTEIN

hetero molecules

Summary:

• 416 kDa, 9 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	415,694	18
Polymers	413,992	9
Non-polymers	1,702	9
Water	16,862	936

1

A: L-SHAPED TAIL FIBER PROTEIN

B: L-SHAPED TAIL FIBER PROTEIN

C: L-SHAPED TAIL FIBER PROTEIN

hetero molecules

Summary:

• defined by author&software
• 139 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	138,565	6
Polymers	137,997	3
Non-polymers	567	3
Water	54	3

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	51540 Å2
ΔGint	-251.6 kcal/mol
Surface area	37930 Å2
Method	PISA

2

D: L-SHAPED TAIL FIBER PROTEIN

E: L-SHAPED TAIL FIBER PROTEIN

F: L-SHAPED TAIL FIBER PROTEIN

hetero molecules

Summary:

• defined by author&software
• 139 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	138,565	6
Polymers	137,997	3
Non-polymers	567	3
Water	54	3

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	51490 Å2
ΔGint	-247.2 kcal/mol
Surface area	37880 Å2
Method	PISA

3

G: L-SHAPED TAIL FIBER PROTEIN

H: L-SHAPED TAIL FIBER PROTEIN

I: L-SHAPED TAIL FIBER PROTEIN

hetero molecules

Summary:

• defined by author&software
• 139 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	138,565	6
Polymers	137,997	3
Non-polymers	567	3
Water	54	3

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	51300 Å2
ΔGint	-251.6 kcal/mol
Surface area	38080 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	160.850, 99.290, 286.230
Angle α, β, γ (deg.)	90.00, 91.51, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	I-991- PHE
2	1	G-2003- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	B
2	9	C
1	10	B
2	10	D
1	11	B
2	11	E
1	12	B
2	12	F
1	13	B
2	13	G
1	14	B
2	14	H
1	15	B
2	15	I
1	16	C
2	16	D
1	17	C
2	17	E
1	18	C
2	18	F
1	19	C
2	19	G
1	20	C
2	20	H
1	21	C
2	21	I
1	22	D
2	22	E
1	23	D
2	23	F
1	24	D
2	24	G
1	25	D
2	25	H
1	26	D
2	26	I
1	27	E
2	27	F
1	28	E
2	28	G
1	29	E
2	29	H
1	30	E
2	30	I
1	31	F
2	31	G
1	32	F
2	32	H
1	33	F
2	33	I
1	34	G
2	34	H
1	35	G
2	35	I
1	36	H
2	36	I

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 989 - 1396 / Label seq-ID: 20 - 427

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	B	B
2	9	C	C
1	10	B	B
2	10	D	D
1	11	B	B
2	11	E	E
1	12	B	B
2	12	F	F
1	13	B	B
2	13	G	G
1	14	B	B
2	14	H	H
1	15	B	B
2	15	I	I
1	16	C	C
2	16	D	D
1	17	C	C
2	17	E	E
1	18	C	C
2	18	F	F
1	19	C	C
2	19	G	G
1	20	C	C
2	20	H	H
1	21	C	C
2	21	I	I
1	22	D	D
2	22	E	E
1	23	D	D
2	23	F	F
1	24	D	D
2	24	G	G
1	25	D	D
2	25	H	H
1	26	D	D
2	26	I	I
1	27	E	E
2	27	F	F
1	28	E	E
2	28	G	G
1	29	E	E
2	29	H	H
1	30	E	E
2	30	I	I
1	31	F	F
2	31	G	G
1	32	F	F
2	32	H	H
1	33	F	F
2	33	I	I
1	34	G	G
2	34	H	H
1	35	G	G
2	35	I	I
1	36	H	H
2	36	I	I

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36

Components

#1: Protein

A B C D E F G H I
L-SHAPED TAIL FIBER PROTEIN

Details:

Mass: 45999.109 Da / Num. of mol.: 9
Fragment: C-TERMINAL DOMAIN WITH INTRAMOLECULAR CHAPERONE, RESIDUES 970-1396
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE T5 (virus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13390

#2: Chemical

A-2397 B-2397 C-2397 D-2397 E-2397 F-2397 G-2397 H-2397 I-2397
ChemComp-FLC / CITRATE ANION

Details:

Mass: 189.100 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₆H₅O₇

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H₂O

• Sequence details: SERINE 1264 WAS MUTATED TO ALANINE TO PREVENT AUTO- PROTEOLYTIC CLEAVAGE

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.8 ų/Da / Density % sol: 55.5 % / Description: NONE
• Crystal grow: pH: 4 ; Details: 10 MM TRIS-HCL, 0.1 M SODIUM CITRATE PH 4.0, 12.5 % (W/V) PEG 2000

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0972
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2013; Details: VERTICAL FOCUSING MIRROR AND HORIZONTAL FOCUSING MIRROR ORTHOGONAL IN A KIRKPATRICK-BAEZ CONFIGURATION
• Radiation: Monochromator: CRYOGENICALLY COOLED CHANNEL-CUT DCM SI (111); Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.0972 Å / Relative weight: 1
• Reflection: Resolution: 2.52→95.4 Å / Num. obs: 150772 / % possible obs: 98.8 % / Redundancy: 4.1 % / B_iso Wilson estimate: 48.4 Ų / R_merge(I) obs: 0.14 / Net I/σ(I): 6.3
• Reflection shell: Resolution: 2.52→2.65 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 3.5 / % possible all: 97.2

Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UW7

4uw7

Resolution: 2.52→95.38 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.911 / SU B: 9.808 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.21311	2061	1.4 %	THIN SHELLS
Rwork	0.18455	-	-	-
obs	0.18497	148385	98.47 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 43.689 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.65 Å2	0 Å2	0.53 Å2
2-	-	-0.15 Å2	0 Å2
3-	-	-	-0.52 Å2

Refinement step

Cycle: LAST / Resolution: 2.52→95.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27442	0	117	936	28495

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	28393
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	26128
X-RAY DIFFRACTION	r_angle_refined_deg	1.397	1.944	38573
X-RAY DIFFRACTION	r_angle_other_deg	1.1	3	60122
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.808	5	3628
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.486	23.362	1261
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.996	15	4391
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.046	15	207
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	4103
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	32863
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	6732
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	5385
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	25203
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	13762
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	14794
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	508
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.143	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.306	0.2	37
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.246	0.2	156
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.136	0.2	6
X-RAY DIFFRACTION	r_symmetry_hbond_other	0.136	0.2	6
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.661	4.198	14452
X-RAY DIFFRACTION	r_mcbond_other	2.66	4.197	14451
X-RAY DIFFRACTION	r_mcangle_it	4.137	6.281	18043
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.097	4.607	13941
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.944	6.761	20511
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	20034	0.06
1	2	B	20034	0.06
2	1	A	19905	0.06
2	2	C	19905	0.06
3	1	A	20094	0.05
3	2	D	20094	0.05
4	1	A	19974	0.06
4	2	E	19974	0.06
5	1	A	19944	0.06
5	2	F	19944	0.06
6	1	A	19880	0.06
6	2	G	19880	0.06
7	1	A	19987	0.06
7	2	H	19987	0.06
8	1	A	19825	0.06
8	2	I	19825	0.06
9	1	B	19844	0.06
9	2	C	19844	0.06
10	1	B	19918	0.05
10	2	D	19918	0.05
11	1	B	19865	0.06
11	2	E	19865	0.06
12	1	B	19855	0.06
12	2	F	19855	0.06
13	1	B	19745	0.06
13	2	G	19745	0.06
14	1	B	19937	0.06
14	2	H	19937	0.06
15	1	B	19790	0.06
15	2	I	19790	0.06
16	1	C	19803	0.06
16	2	D	19803	0.06
17	1	C	19992	0.05
17	2	E	19992	0.05
18	1	C	19905	0.06
18	2	F	19905	0.06
19	1	C	19722	0.06
19	2	G	19722	0.06
20	1	C	19895	0.06
20	2	H	19895	0.06
21	1	C	19888	0.06
21	2	I	19888	0.06
22	1	D	19933	0.06
22	2	E	19933	0.06
23	1	D	19919	0.06
23	2	F	19919	0.06
24	1	D	19946	0.05
24	2	G	19946	0.05
25	1	D	19930	0.06
25	2	H	19930	0.06
26	1	D	19877	0.06
26	2	I	19877	0.06
27	1	E	19819	0.06
27	2	F	19819	0.06
28	1	E	19743	0.07
28	2	G	19743	0.07
29	1	E	19939	0.06
29	2	H	19939	0.06
30	1	E	19932	0.06
30	2	I	19932	0.06
31	1	F	19802	0.06
31	2	G	19802	0.06
32	1	F	19887	0.07
32	2	H	19887	0.07
33	1	F	19819	0.06
33	2	I	19819	0.06
34	1	G	19834	0.07
34	2	H	19834	0.07
35	1	G	19731	0.07
35	2	I	19731	0.07
36	1	H	19881	0.06
36	2	I	19881	0.06

LS refinement shell

Resolution: 2.518→2.654 Å / Total num. of bins used: 10

	Rfactor	Num. reflection	% reflection
Rfree	0.29	312	-
Rwork	0.278	21161	-
obs	-	-	96.8 %