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- PDB-6p20: Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a... -

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Basic information

Entry
Database: PDB / ID: 6p20
TitleBacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix fragment modified to mimic the phiKZ central spike gp164
Components
  • Baseplate central spike complex protein gp5,PHIKZ164
  • PAAR-repeat central spike tip protein
KeywordsVIRAL PROTEIN / bacteriophage / phiKZ / membrane piercing / central spike / cell puncturing device / PAAR-repeat motif / beta helix / T4 gp5 / Pseudomonas aeruginosa / contractile injection system
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding
Similarity search - Function
Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
9-OCTADECENOIC ACID / PALMITIC ACID / STEARIC ACID / PHIKZ163.1 / Pre-baseplate central spike protein Gp5 / PHIKZ164
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Pseudomonas phage phiKZ (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å
AuthorsButh, S.A. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_144243 Switzerland
Citation
Journal: To Be Published
Title: Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix fragment modified to mimic the phiKZ central spike gp164
Authors: Buth, S.A. / Shneider, M.M. / Leiman, P.G.
#1: Journal: Nature / Year: 2013
Title: PAAR-repeat proteins sharpen and diversify the type VI secretion system spike.
Authors: Shneider, M.M. / Buth, S.A. / Ho, B.T. / Basler, M. / Mekalanos, J.J. / Leiman, P.G.
#2: Journal: Viruses / Year: 2015
Title: Structure and Biophysical Properties of a Triple-Stranded Beta-Helix Comprising the Central Spike of Bacteriophage T4.
Authors: Buth, S.A. / Menin, L. / Shneider, M.M. / Engel, J. / Boudko, S.P. / Leiman, P.G.
History
DepositionMay 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baseplate central spike complex protein gp5,PHIKZ164
B: Baseplate central spike complex protein gp5,PHIKZ164
C: Baseplate central spike complex protein gp5,PHIKZ164
D: PAAR-repeat central spike tip protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,60812
Polymers43,5844
Non-polymers1,0248
Water10,701594
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29800 Å2
ΔGint-95 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.427, 66.597, 173.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Baseplate central spike complex protein gp5,PHIKZ164 / Peptidoglycan hydrolase gp5 / Protein Gp5


Mass: 11591.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Pseudomonas phage phiKZ (virus)
Gene: 5, PHIKZ164 / Plasmid: PEEVA2 / Details (production host): a PET-23A DERIVATIVE / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: P16009, UniProt: Q8SCZ8, lysozyme
#2: Protein PAAR-repeat central spike tip protein


Mass: 8809.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiKZ (virus) / Plasmid: pATE / Details (production host): A PACYCDUET-1 DERIVATIVE / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: L7T0L4

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Non-polymers , 7 types, 602 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#5: Chemical ChemComp-ELA / 9-OCTADECENOIC ACID / Elaidic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsT4 gp5 beta helix fragment modified at the C-terminus to mimic gp164 of phiKZ phage. Chimera ...T4 gp5 beta helix fragment modified at the C-terminus to mimic gp164 of phiKZ phage. Chimera consists of a T4 gp5 fragment G484-S559 extended by a K262-T293 C-terminal fragment from phiKZ gp164

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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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-30% PEG 3350 100 mM MES ph 6.5 200-350 mM Mg(NO3)2
PH range: 6-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 20, 2013 / Details: MIRRORS
RadiationMonochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS (DCCM) IN (+--+) GEOMETRY AND A TOROIDAL MIRROR (M2)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.749→50 Å / Num. obs: 77426 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.89 Å2 / CC1/2: 1 / Rrim(I) all: 0.055 / Net I/σ(I): 18.17
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.63 / Num. unique obs: 12230 / CC1/2: 0.807 / Rrim(I) all: 0.552 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSMarch 30, 2013data reduction
XDSMarch 30, 2013data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJ2

4jj2


Resolution: 1.749→36.384 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.1
RfactorNum. reflection% reflection
Rfree0.1914 2691 3.48 %
Rwork0.1477 --
obs0.1492 77378 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.53 Å2
Refinement stepCycle: LAST / Resolution: 1.749→36.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 66 594 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033294
X-RAY DIFFRACTIONf_angle_d0.6434469
X-RAY DIFFRACTIONf_dihedral_angle_d11.2131950
X-RAY DIFFRACTIONf_chiral_restr0.052509
X-RAY DIFFRACTIONf_plane_restr0.004586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7491-1.78090.32921330.27893651X-RAY DIFFRACTION93
1.7809-1.81510.28781450.22873983X-RAY DIFFRACTION100
1.8151-1.85220.22711420.2133876X-RAY DIFFRACTION99
1.8522-1.89240.22131420.18233994X-RAY DIFFRACTION100
1.8924-1.93640.21691450.16393907X-RAY DIFFRACTION100
1.9364-1.98490.2041470.15383970X-RAY DIFFRACTION100
1.9849-2.03850.21181440.15613958X-RAY DIFFRACTION100
2.0385-2.09850.18291410.14773883X-RAY DIFFRACTION100
2.0985-2.16620.2171460.14054015X-RAY DIFFRACTION100
2.1662-2.24360.16781410.13953944X-RAY DIFFRACTION100
2.2436-2.33350.18331480.1343978X-RAY DIFFRACTION100
2.3335-2.43960.2011460.143949X-RAY DIFFRACTION100
2.4396-2.56820.19391380.14183920X-RAY DIFFRACTION100
2.5682-2.72910.18611400.14143976X-RAY DIFFRACTION100
2.7291-2.93970.16171440.1323931X-RAY DIFFRACTION100
2.9397-3.23540.20121350.13893963X-RAY DIFFRACTION100
3.2354-3.70320.19911370.12423964X-RAY DIFFRACTION100
3.7032-4.66410.16051320.12033903X-RAY DIFFRACTION99
4.6641-36.39230.17521450.18223922X-RAY DIFFRACTION99
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)
13.31390.3677-0.61430.339-0.18880.16270.0966-0.34760.2727-0.0313-0.01940.11440.3197-0.04090.02380.4338-0.01350.0170.32820.05710.19458.3349-18.9198-7.419
20.38860.12840.08590.4074-0.01040.46190.07-0.0132-0.02080.0797-0.26440.03470.2214-0.0308-0.27190.32910.0020.11490.23380.00530.1913-7.6995-18.0433-13.5789
30.1281-0.11580.05830.30610.23780.4429-0.0247-0.0082-0.02530.10840.03740.00090.10180.0148-0.00010.2095-0.00350.06340.1987-0.0110.21060.3666-17.5869-31.8158
40.05450.0018-0.00410.0324-0.04410.05930.00370.0831-0.1033-0.1085-0.0639-0.02940.12420.068600.2234-0.01440.0640.2071-0.01290.18265.2372-14.5771-49.4614
50.0366-0.0066-0.00470.03210.00930.0343-0.0533-0.00820.0836-0.06780.00780.00220.1334-0.0772-0.00050.1944-0.00370.04640.1922-0.03190.219-2.7829-26.9376-54.9718
60.033-0.00660.05460.05230.01340.0998-0.0750.0173-0.0156-0.07630.06070.0443-0.00910.0262-0.00120.1782-0.01560.05980.2039-0.01330.19212.0909-21.5395-65.1711
70.0001-0.00520.00220.2439-0.10120.042-0.0677-0.20410.11650.3075-0.0464-0.08680.31210.2181-0.00190.24890.0220.06930.2768-0.02930.1863-0.6174-6.0793-9.4016
80.0474-0.0164-0.00970.00830.00810.00970.1422-0.193-0.26820.2255-0.07440.02530.3690.1638-0.00010.42930.01470.040.30560.03370.28075.257-23.2757-13.2466
90.0945-0.0984-0.08470.181-0.00390.17570.0198-0.1962-0.05390.1442-0.00680.04310.07490.052200.2268-0.00740.05880.21780.00920.21720.7995-14.5832-23.6401
100.53760.2807-0.02180.1659-0.01320.0002-0.10490.11170.0598-0.0170.007-0.13060.29350.0132-0.03580.25050.03430.04870.2113-0.02950.1794-4.1768-24.2166-31.0894
110.4643-0.1534-0.10170.1678-0.01050.1202-0.1242-0.20280.132-0.00910.0136-0.07940.0587-0.0083-0.08220.1633-0.00270.0720.2084-0.01950.21921.0962-10.9586-38.6213
120.01320.005-0.01720.0073-0.01870.0474-0.0954-0.04690.0167-0.10990.1013-0.14190.07660.0143-00.24110.00930.05530.1835-0.02640.25254.5341-24.8487-42.9351
130.04750.01870.02810.00660.01080.0162-0.04730.05490.00150.17980.08460.08740.008-0.1571-00.233-0.02520.04140.2511-0.02660.2427-5.0067-15.8932-50.152
140.1321-0.03550.10270.052-0.01650.0815-0.07250.13-0.0080.06380.1132-0.05410.0580.3004-0.0280.23210.00870.04770.202-0.04150.19217.6431-22.1888-56.126
150.048-0.0086-0.05250.0244-0.01250.0776-0.12870.0845-0.14430.1052-0.01460.08530.0704-0.0615-0.00010.2143-0.01190.04130.2495-0.01030.2804-5.9979-24.0528-61.7619
160.03180.01510.01070.0070.00470.0073-0.00640.08550.12050.05440.02910.02470.0737-0.0571-00.1863-0.01210.04970.2075-0.00810.17414.9443-16.364-69.0051
170.34550.01870.10280.1251-0.02020.03530.0573-0.31730.02020.1335-0.0877-0.01280.23190.0224-0.06160.3780.00210.0570.28980.05020.2017-6.68-20.0412-7.696
180.0050.02180.0130.09410.05670.03410.2023-0.042-0.0084-0.0335-0.1007-0.1151-0.0633-0.01350.00010.27340.00390.04510.2847-0.00280.24813.5233-7.875-15.2982
190.05110.0156-0.05950.0084-0.00830.09120.0485-0.0291-0.26530.1281-0.009-0.01540.21550.0491-0.00010.33720.04620.06430.22030.01370.24392.7036-25.5958-18.9094
200.0994-0.02870.0940.1563-0.19820.3734-0.022-0.02850.00780.07670.0464-0.04770.09390.0068-00.2148-0.01710.05790.1828-0.01870.21920.2656-14.672-28.7138
210.0535-0.01160.05740.0504-0.00480.0911-0.05770.2824-0.25840.3332-0.11010.14030.05510.1415-0.00380.257-0.01120.07270.1991-0.0110.2535-6.3695-21.6987-37.4877
220.01380.01430.03520.03340.06320.12450.1038-0.03450.0187-0.1043-0.0065-0.1269-0.13030.041100.1969-0.02190.04690.1566-0.01240.17794.5581-13.0435-44.4834
230.0213-0.00780.01960.02660.01440.03780.09860.20950.22980.0433-0.14410.06580.10150.0345-0.00010.25380.02480.0680.25-0.00330.2945-0.6794-26.3806-49.1911
240.06530.1145-0.05110.24640.03110.34740.01160.0228-0.0101-0.0116-0.0246-0.0135-0.0030.013500.2218-0.01570.04790.2237-0.01940.214-0.7134-20.3729-62.8353
250.0321-0.01-0.03430.0623-0.01070.05040.08360.01680.0270.0813-0.11570.02-0.06520.0162-0.06610.15840.01260.05280.1946-0.0070.1294.7933-26.1393-82.6203
260.16360.0718-0.05750.13170.05840.0897-0.04270.04420.019-0.0246-0.0063-0.0805-0.0596-0.0031-00.1937-0.00510.05370.22080.00610.16494.5382-19.5801-83.4402
270.01770.0068-0.00240.01590.0590.26870.02450.03750.0379-0.0114-0.0564-0.01050.0508-0.0714-0.09620.3279-0.06030.16980.4534-0.07430.26030.0182-25.0233-102.6971
280.0463-0.01990.04440.049-0.00120.0498-0.09890.1792-0.0613-0.0985-0.14940.0467-0.02310.002-0.0010.2083-0.02010.05330.3364-0.01710.2345-4.3778-21.3091-89.1733
290.01430.0151-0.00120.01910.01090.0362-0.03320.04640.0006-0.109-0.1309-0.0518-0.1282-0.098-0.00020.1725-0.010.00570.2073-0.01450.1778-5.188-19.1905-77.051
300.02560.01080.00840.0173-0.00540.02330.01360.0879-0.2626-0.2158-0.17740.07320.1284-0.220.00020.2445-0.01960.0640.2741-0.0690.2462-4.1623-28.8075-84.9552
310.0480.05420.0070.20070.14110.126-0.16910.2166-0.29150.0684-0.0766-0.07210.32850.0062-0.01840.2104-0.01850.05720.2694-0.03630.1964-0.316-29.1663-82.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 482 through 491 )
2X-RAY DIFFRACTION2chain 'A' and (resid 492 through 501 )
3X-RAY DIFFRACTION3chain 'A' and (resid 502 through 551 )
4X-RAY DIFFRACTION4chain 'A' and (resid 552 through 561 )
5X-RAY DIFFRACTION5chain 'A' and (resid 562 through 571 )
6X-RAY DIFFRACTION6chain 'A' and (resid 572 through 591 )
7X-RAY DIFFRACTION7chain 'B' and (resid 483 through 492 )
8X-RAY DIFFRACTION8chain 'B' and (resid 493 through 502 )
9X-RAY DIFFRACTION9chain 'B' and (resid 503 through 522 )
10X-RAY DIFFRACTION10chain 'B' and (resid 523 through 532 )
11X-RAY DIFFRACTION11chain 'B' and (resid 533 through 542 )
12X-RAY DIFFRACTION12chain 'B' and (resid 543 through 552 )
13X-RAY DIFFRACTION13chain 'B' and (resid 553 through 562 )
14X-RAY DIFFRACTION14chain 'B' and (resid 563 through 572 )
15X-RAY DIFFRACTION15chain 'B' and (resid 573 through 582 )
16X-RAY DIFFRACTION16chain 'B' and (resid 583 through 591 )
17X-RAY DIFFRACTION17chain 'C' and (resid 483 through 492 )
18X-RAY DIFFRACTION18chain 'C' and (resid 493 through 502 )
19X-RAY DIFFRACTION19chain 'C' and (resid 503 through 512 )
20X-RAY DIFFRACTION20chain 'C' and (resid 513 through 532 )
21X-RAY DIFFRACTION21chain 'C' and (resid 533 through 542 )
22X-RAY DIFFRACTION22chain 'C' and (resid 543 through 552 )
23X-RAY DIFFRACTION23chain 'C' and (resid 553 through 562 )
24X-RAY DIFFRACTION24chain 'C' and (resid 563 through 591 )
25X-RAY DIFFRACTION25chain 'D' and (resid 2 through 11 )
26X-RAY DIFFRACTION26chain 'D' and (resid 12 through 41 )
27X-RAY DIFFRACTION27chain 'D' and (resid 42 through 46 )
28X-RAY DIFFRACTION28chain 'D' and (resid 47 through 56 )
29X-RAY DIFFRACTION29chain 'D' and (resid 57 through 66 )
30X-RAY DIFFRACTION30chain 'D' and (resid 67 through 71 )
31X-RAY DIFFRACTION31chain 'D' and (resid 72 through 88 )

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