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- PDB-5aq5: Structure of the Carboxy-Terminal Domain of the Bacteriophage T5 ... -

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Basic information

Entry
Database: PDB / ID: 5aq5
TitleStructure of the Carboxy-Terminal Domain of the Bacteriophage T5 L- Shaped Tail Fibre
ComponentsL-SHAPED TAIL FIBER PROTEIN PB8
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


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
Similarity search - Function
Intramolecular chaperone auto-processing domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing (ICA) domain profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Side tail fiber protein pb1 / Side tail fiber protein pb1
Similarity search - Component
Biological speciesESCHERICHIA PHAGE T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGarcia-Doval, C. / Granell, M. / van Raaij, M.J.
CitationJournal: 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.
History
DepositionSep 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-SHAPED TAIL FIBER PROTEIN PB8
B: L-SHAPED TAIL FIBER PROTEIN PB8
C: L-SHAPED TAIL FIBER PROTEIN PB8
D: L-SHAPED TAIL FIBER PROTEIN PB8
E: L-SHAPED TAIL FIBER PROTEIN PB8
F: L-SHAPED TAIL FIBER PROTEIN PB8
G: L-SHAPED TAIL FIBER PROTEIN PB8
H: L-SHAPED TAIL FIBER PROTEIN PB8
I: L-SHAPED TAIL FIBER PROTEIN PB8
J: L-SHAPED TAIL FIBER PROTEIN PB8
K: L-SHAPED TAIL FIBER PROTEIN PB8
L: L-SHAPED TAIL FIBER PROTEIN PB8


Theoretical massNumber of molelcules
Total (without water)413,48712
Polymers413,48712
Non-polymers00
Water15,457858
1
A: L-SHAPED TAIL FIBER PROTEIN PB8
B: L-SHAPED TAIL FIBER PROTEIN PB8
C: L-SHAPED TAIL FIBER PROTEIN PB8


Theoretical massNumber of molelcules
Total (without water)103,3723
Polymers103,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35610 Å2
ΔGint-214.7 kcal/mol
Surface area24960 Å2
MethodPISA
2
D: L-SHAPED TAIL FIBER PROTEIN PB8
E: L-SHAPED TAIL FIBER PROTEIN PB8
F: L-SHAPED TAIL FIBER PROTEIN PB8


Theoretical massNumber of molelcules
Total (without water)103,3723
Polymers103,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35400 Å2
ΔGint-212.7 kcal/mol
Surface area24840 Å2
MethodPISA
3
G: L-SHAPED TAIL FIBER PROTEIN PB8
H: L-SHAPED TAIL FIBER PROTEIN PB8
I: L-SHAPED TAIL FIBER PROTEIN PB8


Theoretical massNumber of molelcules
Total (without water)103,3723
Polymers103,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35390 Å2
ΔGint-210.9 kcal/mol
Surface area24880 Å2
MethodPISA
4
J: L-SHAPED TAIL FIBER PROTEIN PB8
K: L-SHAPED TAIL FIBER PROTEIN PB8
L: L-SHAPED TAIL FIBER PROTEIN PB8


Theoretical massNumber of molelcules
Total (without water)103,3723
Polymers103,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35450 Å2
ΔGint-211.6 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.623, 95.029, 127.748
Angle α, β, γ (deg.)68.24, 70.20, 83.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth seq-ID: 990 - 1263 / Label seq-ID: 55 - 328

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.496966, -0.75477, 0.428192), (0.792203, -0.193216, 0.578863), (-0.354175, 0.62689, 0.693952)79.62507, 22.27469, -13.71885
3given(-0.50095, 0.79051, -0.35234), (-0.752372, -0.196548, 0.628732), (0.427767, 0.580054, 0.693219)17.23924, 73.08784, -37.45229
4given(-0.515924, 0.754467, -0.40571), (0.783516, 0.224147, -0.579536), (-0.346302, -0.616877, -0.70678)29.91119, -64.23843, -12.73404
5given(-0.481175, -0.809776, 0.335757), (-0.760758, 0.195428, -0.618915), (0.435566, -0.553236, -0.710079)107.58967, 51.08952, -73.61925
6given(0.99972, 0.022655, -0.006765), (0.022473, -0.999413, -0.025849), (-0.007347, 0.02569, -0.999643)-44.21111, 54.68492, -70.72798
7given(0.264553, 0.856436, -0.443316), (-0.344454, 0.513288, 0.786058), (0.900757, -0.055252, 0.430795)-63.79435, 69.57909, -14.20215
8given(0.515472, -0.836327, -0.186671), (0.797019, 0.547941, -0.25401), (0.31472, -0.017845, 0.949017)52.79275, -50.04299, 42.5342
9given(-0.722022, -0.006416, 0.69184), (0.437835, -0.778496, 0.449716), (0.535709, 0.627617, 0.5649)109.39558, 98.2277, -34.32628
10given(0.499287, -0.839589, -0.214015), (-0.799878, -0.54159, 0.258602), (-0.333028, 0.04207, -0.941978)52.78648, 151.9415, -1.77669
11given(0.210711, 0.84389, -0.493407), (0.356992, -0.536306, -0.764809), (-0.910032, -0.014989, -0.414267)-61.90518, 33.70916, 61.78873
12given(-0.76378, -0.023904, 0.645034), (-0.430212, 0.763844, -0.481104), (-0.481205, -0.644958, -0.593692)111.59644, 2.61394, 72.05231

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Components

#1: Protein
L-SHAPED TAIL FIBER PROTEIN PB8 / LTF / L-SHAPED TAIL FIBRES


Mass: 34457.211 Da / Num. of mol.: 12 / Fragment: C-TERMINAL DOMAIN, UNP 970-1263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA PHAGE T5 (virus) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q66LT2, UniProt: P13390*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.8 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL PH 8.5, 8% (W/V) PEG 4000, 10 MM IRON(III) CHLORIDE, 20% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
Details: VERTICAL FOCUSING MIRROR AND HORIZONTAL FOCUSING MIRROR ORTHOGONAL IN A KIRKPATRICK-BAEZ CONFIGURATION
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL-CUT DCM SI (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→23 Å / Num. obs: 144381 / % possible obs: 91.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UW7

4uw7


Resolution: 2.3→23 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 25.654 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25228 2906 2 %THIN SHELLS
Rwork0.22297 ---
obs0.22354 140892 90.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å22.03 Å2-2.16 Å2
2--2.54 Å2-1.05 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24486 0 0 858 25344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01925074
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.93834128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12853290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5623.0371034
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.454153688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4815192
X-RAY DIFFRACTIONr_chiral_restr0.080.23698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1670.221792
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.233096
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.21764
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3540.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5962.36513196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0443.54516474
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.622.40111878
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0383.57917654
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2033 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A5.05
2B4.8
3C4.29
4D3.58
5E3.59
6F4.48
7G4.19
8H5.29
9I5.24
10J4.78
11K4.74
12L4.14
LS refinement shellResolution: 2.3→2.423 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 467 -
Rwork0.29 20160 -
obs--89.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.84650.00770.07051.02540.8172.22970.0345-0.08740.11950.03240.0842-0.1414-0.30510.0874-0.11870.30380.01780.07820.2608-0.11180.098532.906740.2135-15.9634
20.8109-0.02030.09350.85710.84292.90960.0259-0.13180.02470.22070.1552-0.20050.12650.2601-0.18110.27210.03450.03170.2875-0.14270.129138.141730.5138-11.0582
30.8983-0.0245-0.07660.99521.02432.8507-0.0082-0.14390.00680.19210.0418-0.02560.0635-0.1196-0.03360.23610.02760.05940.2702-0.09880.065426.195931.448-11.1844
40.94850.07310.50190.82390.72182.6625-0.03490.1623-0.0071-0.22020.1066-0.1239-0.16990.4154-0.07160.2595-0.01340.10290.2254-0.06860.069281.402227.6448-59.4706
50.9750.00610.60890.73350.77182.5873-0.02280.1119-0.0188-0.1661-0.0065-0.0102-0.1837-0.01530.02930.25720.02660.07350.15-0.05080.048569.329726.4409-59.2961
61.2305-0.17250.29491.18661.06272.35250.10830.086-0.196-0.01940.0981-0.10630.22120.182-0.20630.25540.03430.0470.1184-0.05370.079976.375917.613-54.9051
71.14880.01230.95521.13020.16462.1834-0.1869-0.25720.1821-0.1065-0.07610.3203-0.4032-0.52080.2630.63420.1712-0.11740.4368-0.13150.400334.158467.8411-66.7264
81.9014-0.11761.45071.02830.01552.3294-0.17230.1010.2048-0.2068-0.03040.1692-0.3755-0.07410.20260.63610.0825-0.08260.3077-0.06790.27843.312367.1387-74.7314
91.745-0.12881.61360.9486-0.06352.98250.0001-0.079-0.0622-0.1458-0.00520.2172-0.0827-0.33340.00510.51020.0926-0.04750.2679-0.07180.339.674357.1917-68.6463
101.47310.54551.60011.31370.93052.6217-0.1452-0.21490.1020.02350.08730.0457-0.1754-0.3220.05790.67360.1132-0.0340.451-0.09340.299484.120476.6157-11.2672
111.36970.3431.35640.95710.62652.6504-0.20290.13930.103-0.12430.2336-0.0766-0.33690.2283-0.03070.71290.0189-0.03210.4409-0.12550.348593.000977.6712-19.5246
121.39210.18231.21880.93720.45422.1726-0.4121-0.00960.3501-0.20260.16370.044-0.6235-0.03620.24840.87980.0605-0.1330.4696-0.12890.466886.251687.3437-16.6018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A989 - 1263
2X-RAY DIFFRACTION2B988 - 1263
3X-RAY DIFFRACTION3C988 - 1263
4X-RAY DIFFRACTION4D989 - 1263
5X-RAY DIFFRACTION5E989 - 1263
6X-RAY DIFFRACTION6F989 - 1263
7X-RAY DIFFRACTION7G989 - 1263
8X-RAY DIFFRACTION8H989 - 1263
9X-RAY DIFFRACTION9I989 - 1263
10X-RAY DIFFRACTION10J989 - 1263
11X-RAY DIFFRACTION11K989 - 1263
12X-RAY DIFFRACTION12L989 - 1263

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