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- PDB-3foa: Crystal structure of the bacteriophage T4 tail sheath protein, de... -

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Basic information

Entry
Database: PDB / ID: 3foa
TitleCrystal structure of the bacteriophage T4 tail sheath protein, deletion mutant gp18M
ComponentsTail sheath protein Gp18
KeywordsVIRAL PROTEIN / alpha-beta / viral structural protein / bacteriophage T4 / tail sheath
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism
Similarity search - Function
Rossmann fold - #11780 / Thrombin, subunit H - #380 / : / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / : / Tail sheath protein, subtilisin-like domain ...Rossmann fold - #11780 / Thrombin, subunit H - #380 / : / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Thrombin, subunit H / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsAksyuk, A.A. / Leiman, P.G. / Kurochkina, L.P. / Shneider, M.M. / Kostyuchenko, V.A. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: EMBO J / Year: 2009
Title: The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria.
Authors: Anastasia A Aksyuk / Petr G Leiman / Lidia P Kurochkina / Mikhail M Shneider / Victor A Kostyuchenko / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The contractile tail of bacteriophage T4 is a molecular machine that facilitates very high viral infection efficiency. Its major component is a tail sheath, which contracts during infection to less ...The contractile tail of bacteriophage T4 is a molecular machine that facilitates very high viral infection efficiency. Its major component is a tail sheath, which contracts during infection to less than half of its initial length. The sheath consists of 138 copies of the tail sheath protein, gene product (gp) 18, which surrounds the central non-contractile tail tube. The contraction of the sheath drives the tail tube through the outer membrane, creating a channel for the viral genome delivery. A crystal structure of about three quarters of gp18 has been determined and was fitted into cryo-electron microscopy reconstructions of the tail sheath before and after contraction. It was shown that during contraction, gp18 subunits slide over each other with no apparent change in their structure.
History
DepositionDec 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail sheath protein Gp18
B: Tail sheath protein Gp18
C: Tail sheath protein Gp18
D: Tail sheath protein Gp18


Theoretical massNumber of molelcules
Total (without water)218,5844
Polymers218,5844
Non-polymers00
Water00
1
A: Tail sheath protein Gp18


Theoretical massNumber of molelcules
Total (without water)54,6461
Polymers54,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tail sheath protein Gp18


Theoretical massNumber of molelcules
Total (without water)54,6461
Polymers54,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tail sheath protein Gp18


Theoretical massNumber of molelcules
Total (without water)54,6461
Polymers54,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tail sheath protein Gp18


Theoretical massNumber of molelcules
Total (without water)54,6461
Polymers54,6461
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.590, 116.290, 433.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D and (resid 30:85 or resid 350:429 or resid 441:479)
21chain B and (resid 30:85 or resid 350:429 or resid 441:479)
31chain C and (resid 30:85 or resid 350:429 or resid 441:479)
41chain A and (resid 30:85 or resid 350:429 or resid 441:479)
12chain D and (resid 190:340)
22chain B and (resid 190:340)
32chain C and (resid 190:340)
13chain D and (resid 190:340)
23chain A and (resid 190:340)
14chain D and (resid 100:170)
24chain A and (resid 100:170)
34chain B and (resid 100:170)
44chain C and (resid 100:170)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAASPASPDD30 - 8530 - 85
121VALVALTRPTRPDD350 - 429350 - 429
131PHEPHEALAALADD441 - 479441 - 479
211ALAALAASPASPBB30 - 8530 - 85
221VALVALTRPTRPBB350 - 429350 - 429
231PHEPHEALAALABB441 - 479441 - 479
311ALAALAASPASPCC30 - 8530 - 85
321VALVALTRPTRPCC350 - 429350 - 429
331PHEPHEALAALACC441 - 479441 - 479
411ALAALAASPASPAA30 - 8530 - 85
421VALVALTRPTRPAA350 - 429350 - 429
431PHEPHEALAALAAA441 - 479441 - 479
112ASPASPLEULEUDD190 - 340190 - 340
212ASPASPLEULEUBB190 - 340190 - 340
312ASPASPLEULEUCC190 - 340190 - 340
113ASPASPLEULEUDD190 - 340190 - 340
213ASPASPLEULEUAA190 - 340190 - 340
114GLUGLUGLUGLUDD100 - 170100 - 170
214GLUGLUGLUGLUAA100 - 170100 - 170
314GLUGLUGLUGLUBB100 - 170100 - 170
414GLUGLUGLUGLUCC100 - 170100 - 170

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Tail sheath protein Gp18


Mass: 54645.965 Da / Num. of mol.: 4 / Fragment: deletion mutant gp18M: UNP Residues 1-510 / Mutation: R510P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 18, GB AAA32541 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13332
Sequence detailsAUTHORS STATE THAT THE SEQUENCE COMPLETELY AGREES WITH THE GENBANK ENTRY AAA32541, PUBMED REPORT 2964531

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 20000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 32322 / % possible obs: 87.77 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.106 / Χ2: 1.425 / Net I/σ(I): 11.905
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.291 / Num. unique all: 1947 / Χ2: 1.112 / % possible all: 61.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FO8

3fo8


Resolution: 3.5→49.795 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.756 / SU ML: 0.59 / σ(F): 1.34 / Stereochemistry target values: MLHL / Details: 3 TLS groups per monomer were used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1408 4.96 %RANDOM
Rwork0.267 ---
all0.269 32322 --
obs0.2687 28369 87.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.38 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 417.78 Å2 / Biso mean: 95.167 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--11.635 Å20 Å2-0 Å2
2--33.758 Å20 Å2
3----22.123 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14406 0 0 0 14406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514666
X-RAY DIFFRACTIONf_angle_d0.98519942
X-RAY DIFFRACTIONf_chiral_restr0.0662300
X-RAY DIFFRACTIONf_plane_restr0.0042596
X-RAY DIFFRACTIONf_dihedral_angle_d18.6835144
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D1352X-RAY DIFFRACTIONPOSITIONAL
12B1352X-RAY DIFFRACTIONPOSITIONAL0.024
13C1352X-RAY DIFFRACTIONPOSITIONAL0.021
14A1352X-RAY DIFFRACTIONPOSITIONAL0.022
21D1140X-RAY DIFFRACTIONPOSITIONAL
22B1140X-RAY DIFFRACTIONPOSITIONAL0.024
23C1140X-RAY DIFFRACTIONPOSITIONAL0.022
31D1140X-RAY DIFFRACTIONPOSITIONAL
32A1140X-RAY DIFFRACTIONPOSITIONAL0.018
41D540X-RAY DIFFRACTIONPOSITIONAL
42A540X-RAY DIFFRACTIONPOSITIONAL0.019
43B540X-RAY DIFFRACTIONPOSITIONAL0.021
44C540X-RAY DIFFRACTIONPOSITIONAL0.021
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.6250.3721050.3461932203764
3.625-3.770.3781050.3452248235375
3.77-3.9420.3181430.3172464260782
3.942-4.1490.3411470.2862729287690
4.149-4.4090.2871480.2522841298994
4.409-4.7490.3211510.2372921307295
4.749-5.2270.2541510.2422925307696
5.227-5.9820.2831420.232958310096
5.982-7.5330.2631670.2282948311595
7.533-49.80.2391490.2172995314492
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)
12.2625-1.8060.66960.811-0.82044.54980.12350.5516-0.476-0.0624-0.3794-0.4265-0.36242.1289-0.10670.5749-0.3716-0.18481.1890.11770.39169.877547.1625-125.2979
22.60260.7664-1.0461-0.33421.81042.52830.42910.1187-0.1352-0.2828-0.4666-0.28940.35040.08450.00450.226-0.077-0.0220.24060.21410.4152-20.86624.6324-31.5817
31.14780.61880.34865.82832.03631.1994-0.00850.42770.2044-0.6178-0.18760.1989-0.562-0.60220.00020.66490.3207-0.20690.6842-0.08740.44439.0417-36.5609-75.1572
42.821-0.97630.42731.5957-0.88932.22550.05580.063-0.0323-0.236-0.03810.3923-0.18120.1438-0.020.24450.04280.06230.29540.11850.182942.147112.071916.8198
50.77470.36123.14430.45520.47492.38791.24861.8814-1.2447-0.17610.0405-0.50221.59812.06730.07881.251.0703-0.61851.8522-0.60171.212626.912622.2119-106.0763
63.99051.86641.31330.23080.39481.14130.1047-0.0024-0.52940.1180.13140.11840.0798-0.44660.00080.39630.12090.05840.21910.04860.46233.665516.0358-55.3748
71.4872-0.2018-0.54451.9932-0.90051.53360.15810.20930.05020.048-0.07140.0516-0.11420.18960.00010.51330.2087-0.09120.32430.00410.453919.6068-10.4901-52.7425
83.3625-2.69480.94061.08630.28213.12-0.002-0.242-0.03380.17130.1060.0851-0.121-0.1543-0.00010.48480.01760.02490.33330.07010.466414.113923.994-2.2496
91.621-1.56720.03793.5880.54242.79670.326-0.6649-1.60470.07441.0290.31851.05360.27941.77290.72830.3488-0.32080.79980.10840.682221.875425.1601-80.9939
101.5842-1.16871.01960.40980.00432.0317-0.07330.6789-0.46010.14950.0211-0.36690.05510.9033-0.34260.54650.4221-0.04450.6865-0.24070.5059-2.84547.1593-78.756
11-0.13820.2668-1.9710.35770.7722-0.2633-0.016-0.01890.47030.7877-0.27910.4723-0.3849-0.285400.69410.1139-0.0720.79310.02970.615912.6602-16.4084-28.7285
12-0.3104-0.67810.72921.2515-2.55410.7410.02140.33160.03720.23590.0429-0.0028-0.0968-0.36300.5016-0.01810.07960.52130.08390.405917.793719.5399-27.331
130.5361-0.3671.8132-0.3135-0.73595.38460.15640.5718-0.18840.2379-0.3530.85630.67991.23820.05490.3233-0.20540.00890.36690.09150.635-5.553944.5834-134.5904
141.8671-0.395-2.93211.02941.05526.6844-0.5058-1.00011.3844-0.185-0.36571.26251.00031.2862-0.71210.3824-0.1535-0.22560.4828-0.14290.3266-34.058914.8163-24.6509
152.81651.0701-1.22374.23582.43466.77170.908-0.6133-0.7762-0.8141-0.4888-1.2805-2.1721-1.45930.38010.65290.3117-0.17360.39940.03150.337719.2034-49.7905-82.5481
167.8677-6.789-1.10336.92-2.78821.1787-1.2853-0.5229-1.52420.66420.2355-0.4747-0.7643-0.7405-2.71870.08870.3255-0.03990.0838-0.02590.435643.8558-2.877726.1625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 24:87 or resid 346:484)
2X-RAY DIFFRACTION2chain B and (resid 22:87 or resid 346:484)
3X-RAY DIFFRACTION3chain C and (resid 23:87 or resid 346:484)
4X-RAY DIFFRACTION4chain D and (resid 18:87 or resid 346:484)
5X-RAY DIFFRACTION5chain A and (resid 88:97 or resid 189:345)
6X-RAY DIFFRACTION6chain B and (resid 88:97 or resid 189:345)
7X-RAY DIFFRACTION7chain C and (resid 88:97 or resid 189:345)
8X-RAY DIFFRACTION8chain D and (resid 88:97 or resid 189:345)
9X-RAY DIFFRACTION9chain A and (resid 98:188)
10X-RAY DIFFRACTION10chain B and (resid 98:188)
11X-RAY DIFFRACTION11chain C and (resid 98:188)
12X-RAY DIFFRACTION12chain D and (resid 98:188)
13X-RAY DIFFRACTION13chain A and (resid 496:)
14X-RAY DIFFRACTION14chain B and (resid 496:)
15X-RAY DIFFRACTION15chain C and (resid 496:)
16X-RAY DIFFRACTION16chain D and (resid 496:)

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