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- PDB-6p22: Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 i... -

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Basic information

Entry
Database: PDB / ID: 6p22
TitlePhotorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC
Components
  • CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
  • PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN
KeywordsVIRAL PROTEIN / PVC / Photorhabdus laumondii / membrane piercing / central spike / cell puncturing device / PAAR-repeat motif / beta helix / T4 gp5 / contractile injection system / Pvc8 / Pvc10 / hydrolase
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
Contractile injection system spike tip protein / Contractile injection system spike tip protein / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain ...Contractile injection system spike tip protein / Contractile injection system spike tip protein / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
9-OCTADECENOIC ACID / PALMITIC ACID / STEARIC ACID / Pre-baseplate central spike protein Gp5 / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17 / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Photorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 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: Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Jul 23, 2025Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
B: CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
C: CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
D: PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5538
Polymers44,7064
Non-polymers8484
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25840 Å2
ΔGint-77 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.305, 56.963, 222.994
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 CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC / T4 CELL-PUNCTURING DEVICE PROTEIN GP5 / PVC CENTRAL SPIKE PROTEIN PVC8


Mass: 10011.937 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Plasmid: PEEVA2 / Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu1723 / Details (production host): a PET-23A DERIVATIVE / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: P16009, UniProt: Q7N647, lysozyme
#2: Protein PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN


Mass: 14669.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu1721 / Variant: TT01 / Plasmid: pATE / Details (production host): A PACYCDUET-1 DERIVATIVE / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: Q7N648

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Non-polymers , 5 types, 145 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-STE / STEARIC ACID


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


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
Sequence detailsT4 gp5 beta helix fragment with a modified C-terminus to mimic the PluTT01m_08915 PVC central spike ...T4 gp5 beta helix fragment with a modified C-terminus to mimic the PluTT01m_08915 PVC central spike protein Pvc8. Chimera consists of a T4 gp5 fragment G484-Y565 extended by the D523-Q533 C-terminal fragment of Pvc8 protein.

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: MPD 28-34% PEG 2000 8-18% 100 mM Imidazole pH 8.0 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 37669 / % possible obs: 99.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 45.19 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.125 / Net I/σ(I): 9.78
Reflection shellResolution: 2.29→2.43 Å / Mean I/σ(I) obs: 2.05 / Num. unique obs: 5838 / CC1/2: 0.95 / Rrim(I) all: 0.702 / % possible all: 96

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Processing

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

4jj2


Resolution: 2.291→45.213 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 25.36
RfactorNum. reflection% reflection
Rfree0.2224 1891 5.05 %
Rwork0.1819 --
obs0.184 37478 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.2 Å2
Refinement stepCycle: LAST / Resolution: 2.291→45.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 59 141 3284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023186
X-RAY DIFFRACTIONf_angle_d0.4834311
X-RAY DIFFRACTIONf_dihedral_angle_d11.1861898
X-RAY DIFFRACTIONf_chiral_restr0.051508
X-RAY DIFFRACTIONf_plane_restr0.003559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2907-2.34790.32861200.28122238X-RAY DIFFRACTION90
2.3479-2.41140.34921360.26452552X-RAY DIFFRACTION99
2.4114-2.48240.25351350.26212607X-RAY DIFFRACTION99
2.4824-2.56250.27461400.24812553X-RAY DIFFRACTION100
2.5625-2.65410.2591360.23032574X-RAY DIFFRACTION100
2.6541-2.76030.32251370.2272517X-RAY DIFFRACTION100
2.7603-2.88590.28371390.21872616X-RAY DIFFRACTION100
2.8859-3.0380.2491360.20342537X-RAY DIFFRACTION100
3.038-3.22830.23961340.18952560X-RAY DIFFRACTION100
3.2283-3.47750.22111420.16282599X-RAY DIFFRACTION100
3.4775-3.82730.20821360.1412556X-RAY DIFFRACTION99
3.8273-4.38070.18391350.14392578X-RAY DIFFRACTION100
4.3807-5.51770.13911340.13542532X-RAY DIFFRACTION99
5.5177-45.22210.22571310.19072568X-RAY DIFFRACTION100
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)
11.24960.0374-0.24870.152-0.19040.2670.35370.5836-0.5301-0.4257-0.3088-0.22140.4071-0.2247-0.00750.7132-0.0648-0.04320.67060.09560.43136.213267.958218.6718
20.1361-0.01350.13530.0020.02060.2825-0.14910.69510.2873-0.28010.0427-0.0070.01020.1845-0.00080.4639-0.1102-0.07740.42690.05620.4847-1.050563.520930.1664
30.61660.4451-0.09940.66860.54971.1172-0.19030.2350.0129-0.27640.11330.33060.1371-0.0688-0.00050.297-0.0099-0.03890.29640.03870.40194.282165.968242.5752
40.46660.25690.35790.63810.2950.2951-0.1380.05620.3789-0.21140.17220.3877-0.0544-0.14560.00010.2201-0.01330.02620.2607-0.00710.3335.231268.07355.429
50.2732-0.23580.06950.2923-0.04880.1573-0.1309-0.18660.10530.07360.07990.1490.075-0.060700.3734-0.0199-0.0130.3061-0.02310.365515.574467.904262.5276
60.207-0.17320.19340.141-0.16110.2010.27120.28040.1207-0.671-0.10220.16510.54130.30790.00040.5181-0.0783-0.04110.51710.03870.46637.038762.706672.7665
73.336-0.0197-0.5240.5410.65590.85940.01620.80120.3542-0.29570.12350.0222-0.077-0.23390.1740.5161-0.1869-0.06150.59290.05140.31451.335665.557224.1815
80.16860.0838-0.2790.2664-0.30790.5863-0.40360.3412-0.0543-0.12770.21360.21140.27610.0576-0.02370.4503-0.0799-0.03080.43440.00250.5019-0.53660.540335.6133
90.20320.25140.24540.43110.2110.3444-0.15770.1520.1739-0.11710.09910.1923-0.0833-0.0380.00010.327-0.0184-0.03310.43320.05280.44143.218669.15345.0304
100.4715-0.1888-0.4040.3958-0.18650.697-0.0032-0.16270.02780.0315-0.10840.23110.03870.0081-0.00010.22160.0084-0.02660.2351-0.02110.324811.602367.003553.3428
110.2905-0.3264-0.21420.43540.41950.55650.40280.1691-0.2644-0.0909-0.20460.19730.0305-0.1451-00.32390.0281-0.0480.3560.02930.373110.431960.61464.1728
120.10310.02760.12560.21720.09350.20750.10980.26910.3755-0.0422-0.11360.3965-0.4155-0.06420.00090.46720.0158-0.00280.3107-0.03810.390413.765572.964770.6334
131.1683-0.6476-1.96640.7041.15813.3233-0.22360.2812-0.15990.2672-0.0594-0.17590.5139-0.6557-0.28210.4009-0.198-0.16870.6750.05670.5431-5.052676.254521.8569
140.4217-0.2574-0.20210.427-0.20420.4628-0.1470.19120.1509-0.73430.19710.1636-0.04410.0007-0.01250.5227-0.0608-0.08020.4664-0.01720.38070.445562.163626.9656
150.2274-0.16050.01620.38130.38770.5867-0.18730.4219-0.0282-0.46950.2833-0.24230.2717-0.4360.00020.4527-0.0396-0.0540.50690.04510.5336-3.118269.50637.7142
160.8764-0.40320.25120.49370.28580.5603-0.18520.0643-0.0673-0.21760.20820.34420.0023-0.1515-0.00030.3772-0.0462-0.00630.35880.00310.36168.358466.71444.0538
170.54320.2731-0.1980.41940.28220.5982-0.278-0.5079-0.30330.17460.1710.10040.03490.0452-0.00240.30780.01820.00620.312-0.02110.42438.337561.413554.9301
180.2983-0.0986-0.1970.1454-0.18250.64980.06770.11980.25280.40270.0459-0.1322-0.0771-0.0282-0.00060.36030.0065-0.00130.3901-0.0170.371311.621866.019766.7684
190.0062-0.03930.00880.2272-0.01310.0505-0.26170.15670.4422-0.15580.14950.663-0.3948-0.4890.00040.50640.0402-0.02730.4997-0.02430.324512.851867.323187.0178
200.9725-0.02480.57790.76550.79851.190.0399-0.186-0.01970.21510.02120.0527-0.2623-0.5138-0.00010.5344-0.0179-0.01670.4219-0.03480.349619.192268.911792.212
210.0784-0.02760.0690.0293-0.02580.0605-0.0974-0.5008-0.0239-0.26870.3391-0.8250.30290.3369-0.00040.5787-0.03690.0140.5258-0.01330.443626.353366.441789.8684
220.5864-0.17060.61690.0468-0.17620.64110.0981-0.32150.10340.306-0.00650.12460.2886-0.25320.00010.6237-0.0501-0.05580.4550.01610.294622.739664.057999.3978
230.34910.0065-0.05930.08670.22780.59270.0243-0.24310.03050.0282-0.1751-0.07310.130.1845-0.00010.4336-0.031-0.06750.49950.02650.330421.876662.353691.791
240.00150.03010.10660.09950.29211.06580.1608-0.4629-0.13680.21140.13840.07580.2057-0.62780.01670.6082-0.0015-0.02260.5288-0.04450.331220.461263.9841101.3959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 483 through 491 )
2X-RAY DIFFRACTION2chain 'A' and (resid 492 through 511 )
3X-RAY DIFFRACTION3chain 'A' and (resid 512 through 536 )
4X-RAY DIFFRACTION4chain 'A' and (resid 537 through 553 )
5X-RAY DIFFRACTION5chain 'A' and (resid 554 through 567 )
6X-RAY DIFFRACTION6chain 'A' and (resid 568 through 576 )
7X-RAY DIFFRACTION7chain 'B' and (resid 484 through 503 )
8X-RAY DIFFRACTION8chain 'B' and (resid 504 through 518 )
9X-RAY DIFFRACTION9chain 'B' and (resid 519 through 536 )
10X-RAY DIFFRACTION10chain 'B' and (resid 537 through 553 )
11X-RAY DIFFRACTION11chain 'B' and (resid 554 through 567 )
12X-RAY DIFFRACTION12chain 'B' and (resid 568 through 576 )
13X-RAY DIFFRACTION13chain 'C' and (resid 483 through 488 )
14X-RAY DIFFRACTION14chain 'C' and (resid 489 through 506 )
15X-RAY DIFFRACTION15chain 'C' and (resid 507 through 519 )
16X-RAY DIFFRACTION16chain 'C' and (resid 520 through 537 )
17X-RAY DIFFRACTION17chain 'C' and (resid 538 through 553 )
18X-RAY DIFFRACTION18chain 'C' and (resid 554 through 576 )
19X-RAY DIFFRACTION19chain 'D' and (resid 2 through 13 )
20X-RAY DIFFRACTION20chain 'D' and (resid 14 through 49 )
21X-RAY DIFFRACTION21chain 'D' and (resid 50 through 53 )
22X-RAY DIFFRACTION22chain 'D' and (resid 54 through 86 )
23X-RAY DIFFRACTION23chain 'D' and (resid 87 through 107 )
24X-RAY DIFFRACTION24chain 'D' and (resid 108 through 138 )

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