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- PDB-6p1z: Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with t... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6p1z
TitleBacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of the T4 gp5 beta-helical domain
Components
  • Baseplate central spike complex protein gp5
  • PAAR-repeat central spike tip protein
Keywordsviral protein / hydrolase / 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
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Pseudomonas phage phiKZ (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 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 the C-terminal part of the T4 gp5 beta-helical domain
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.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.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

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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
B: Baseplate central spike complex protein gp5
C: Baseplate central spike complex protein gp5
D: PAAR-repeat central spike tip protein
E: Baseplate central spike complex protein gp5
F: Baseplate central spike complex protein gp5
G: Baseplate central spike complex protein gp5
H: PAAR-repeat central spike tip protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,58518
Polymers76,7598
Non-polymers1,82610
Water16,718928
1
A: Baseplate central spike complex protein gp5
B: Baseplate central spike complex protein gp5
C: Baseplate central spike complex protein gp5
D: PAAR-repeat central spike tip protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2929
Polymers38,3794
Non-polymers9135
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24910 Å2
ΔGint-64 kcal/mol
Surface area13440 Å2
MethodPISA
2
E: Baseplate central spike complex protein gp5
F: Baseplate central spike complex protein gp5
G: Baseplate central spike complex protein gp5
H: PAAR-repeat central spike tip protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2929
Polymers38,3794
Non-polymers9135
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25150 Å2
ΔGint-61 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.275, 69.123, 77.802
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ABCEFGDH

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


Mass: 9856.678 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: pEEVA2 / Details (production host): a PET-23A DERIVATIVE / Production host: Escherichia coli (E. coli) / Variant (production host): B834 / References: UniProt: P16009, lysozyme
#2: Protein PAAR-repeat central spike tip protein


Mass: 8809.327 Da / Num. of mol.: 2
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 , 6 types, 938 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2
#6: Chemical ChemComp-ELA / 9-OCTADECENOIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 47.5-50 % PEG5500 MME 100 mM Glycine pH 10 25-100 mM KBr

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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: 2.099→50 Å / Num. obs: 82024 / % possible obs: 95.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 28.16 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.12 / Net I/σ(I): 6.93
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 1.72 % / Mean I/σ(I) obs: 2 / Num. unique obs: 12480 / CC1/2: 0.871 / Rrim(I) all: 0.483 / % possible all: 89.3

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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: 2.099→44.597 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 27.46
RfactorNum. reflection% reflection
Rfree0.2514 2890 3.53 %
Rwork0.1877 --
obs0.19 81765 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.86 Å2
Refinement stepCycle: LAST / Resolution: 2.099→44.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 120 928 6268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025454
X-RAY DIFFRACTIONf_angle_d0.4417381
X-RAY DIFFRACTIONf_dihedral_angle_d10.7593207
X-RAY DIFFRACTIONf_chiral_restr0.051864
X-RAY DIFFRACTIONf_plane_restr0.002959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0995-2.13390.30691230.27213171X-RAY DIFFRACTION80
2.1339-2.17070.331410.2563785X-RAY DIFFRACTION94
2.1707-2.21010.31331310.24713630X-RAY DIFFRACTION93
2.2101-2.25270.33671280.22393620X-RAY DIFFRACTION92
2.2527-2.29860.30441430.23333859X-RAY DIFFRACTION98
2.2986-2.34860.27281410.22963844X-RAY DIFFRACTION99
2.3486-2.40320.33271430.22383877X-RAY DIFFRACTION98
2.4032-2.46330.24631390.22543880X-RAY DIFFRACTION98
2.4633-2.52990.32491420.22673879X-RAY DIFFRACTION99
2.5299-2.60440.30611440.22063907X-RAY DIFFRACTION99
2.6044-2.68840.31831420.2263894X-RAY DIFFRACTION98
2.6884-2.78450.31321420.20343879X-RAY DIFFRACTION97
2.7845-2.8960.26971330.19373768X-RAY DIFFRACTION96
2.896-3.02770.28181350.18573708X-RAY DIFFRACTION94
3.0277-3.18730.2371360.18123676X-RAY DIFFRACTION94
3.1873-3.3870.23351360.16133704X-RAY DIFFRACTION94
3.387-3.64840.21861410.13513884X-RAY DIFFRACTION98
3.6484-4.01530.20741410.14133838X-RAY DIFFRACTION97
4.0153-4.59580.21671390.13823757X-RAY DIFFRACTION96
4.5958-5.78820.15461330.14713676X-RAY DIFFRACTION93
5.7882-44.60750.19781370.21063639X-RAY DIFFRACTION92
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)
11.2174-0.22830.16070.17690.02110.34360.1073-0.51630.1099-0.00520.18030.22220.0535-0.28070.29790.1857-0.01190.02270.1414-0.02150.250558.951-2.908787.9453
20.33610.05150.26650.1402-0.18130.37260.10530.04310.25440.267-0.22630.25720.1672-0.0374-0.00030.21760.0087-0.01910.23790.00220.275567.19050.818879.7402
30.2097-0.03020.13580.0688-0.06180.1227-0.005-0.18460.0741-0.0892-0.0978-0.13970.11340.0102-0.00010.19670.00380.01670.2167-0.00550.220479.1147-3.150180.1376
40.52970.25010.1050.23150.0909-0.11060.032-0.0130.0554-0.0371-0.02770.0095-0.0495-0.05260.01960.1443-0.0022-0.01540.19830.01840.227994.94314.694778.7552
50.1001-0.0931-0.10340.4321-0.12720.16890.0479-0.15350.03080.0835-0.16380.3041-0.0221-0.1155-0.09240.2502-0.03140.00160.2017-0.00720.277959.0537-3.465185.4707
60.2663-0.01960.26380.33590.38230.48290.01710.09790.07980.0271-0.00940.16440.0282-0.076-00.19400.02060.19980.01790.261678.90780.693180.2286
70.0791-0.04910.10110.1032-0.07790.1501-0.0296-0.0366-0.05650.0528-0.17860.3378-0.06650.35480.00130.17520.00670.00480.1532-0.02250.180997.0042-1.08877.7453
80.08450.0845-0.01760.1315-0.0442-0.04590.2117-0.0055-0.23460.0081-0.1419-0.00130.2460.00130.00010.1798-0.01890.01980.2060.01470.239100.975611.285973.1477
90.13360.00940.23850.05710.12690.2083-0.04670.0212-0.03050.0188-0.15430.01680.1046-0.1424-00.2103-0.05350.0090.2660.04440.283359.0537-6.202886.8729
100.5520.34120.00720.5931-0.27080.13680.01770.07320.08140.1009-0.04680.11450.0066-0.097500.1995-0.01420.00520.2268-0.030.240172.25591.341782.1581
111.22491.1205-0.89891.0477-0.83550.66460.3065-0.3760.3650.1879-0.3237-0.2659-0.36640.1766-0.1750.2056-0.00020.00960.1415-0.09050.302883.79983.597787.9987
120.15820.0380.0128-0.06010.01250.0039-0.05430.0019-0.06980.0429-0.06290.18820.4877-0.1728-00.2374-0.00770.02660.21490.0020.213988.3674-5.295379.7454
130.14290.16210.05770.2081-0.00770.1654-0.0240.2045-0.0006-0.22560.21970.3861-0.01960.38210.00160.18470.04880.03770.220.01180.207589.04345.394570.4315
140.03770.01210.21250.2445-0.20181.34290.14970.00890.10840.0557-0.02350.00160.19370.08740.0890.14340.00280.0050.185-0.01190.2483100.32584.075576.1059
151.2653-0.1658-0.40130.2345-0.15960.2631-0.10530.1611-0.3623-0.1279-0.01550.0907-0.0589-0.0413-0.08840.17560.01520.00420.1408-0.00680.156116.09328.153366.7185
160.0708-0.1308-0.43320.19260.67092.77070.05190.4530.15280.1099-0.0029-0.47330.58350.08760.11040.0360.05140.04090.21970.0470.2783132.27098.696766.9295
170.27370.0599-0.1540.0036-0.00140.0601-0.0410.06170.00010.0385-0.0444-0.2051-0.0153-0.006700.17330.0107-0.01280.18970.01920.2153117.3189.757175.7473
180.2825-0.2836-0.23240.5091-0.12110.41320.426-0.51490.02010.0384-0.1646-0.01590.1259-0.13590.08470.3834-0.09010.02750.4234-0.07180.332983.82560.1028125.16
190.82330.06240.16380.16960.20020.17250.1775-0.01630.09190.1437-0.18180.1963-0.00940.06840.00050.2844-0.00990.00980.2652-0.00990.288499.667-2.1795118.6512
202.98360.9522-0.45991.2619-0.55651.94190.8626-0.30230.907-0.0201-0.40990.5794-0.08590.25341.03450.2174-0.0164-0.02450.16610.04420.0088115.98133.2813119.7978
210.3125-0.1331-0.16380.0028-0.00230.26970.06870.19720.3244-0.1195-0.08810.0733-0.13410.12960.02550.23160.02870.01740.28410.07780.3577126.00525.4858112.2239
221.3423-0.08770.45890.8666-0.0910.50410.3611-0.23330.1584-0.0191-0.2270.25750.0290.0080.20820.2616-0.0626-0.01640.3338-0.03350.238789.233-4.915123.5703
231.1421-0.0460.20.14560.04890.19620.22210.06470.35170.0113-0.1653-0.0128-0.0611-0.11820.01910.27030.02640.04360.26740.00870.3563107.41382.5647116.0083
240.64410.28-0.16650.22020.20750.34110.3185-0.07520.26270.0074-0.3086-0.1797-0.29240.2934-0.03680.33480.02840.04490.26160.01570.3327125.84594.3724112.2414
250.9248-0.64221.07650.8957-0.78941.42120.3433-0.3585-0.2025-0.0266-0.0090.32510.2452-0.04670.31010.2331-0.1159-0.00360.34350.00810.304785.6247-6.0078127.7886
261.57840.5120.08870.3788-0.54670.36650.20230.00710.14280.0444-0.12940.1613-0.0805-0.0236-00.29250.00330.01570.2722-0.02510.2387103.63540.0665117.7701
271.806-0.1943-0.24350.9981-0.01382.08070.50220.24290.3413-0.0451-0.1191-0.1796-0.12320.03361.56570.22250.02550.02810.1870.02930.1768125.97714.2424112.8232
280.15910.167-0.06540.48060.25740.1299-0.1160.4770.1494-0.1087-0.0481-0.05280.06080.1057-0.03720.24770.04750.01750.40310.04310.2491142.94156.4418103.387
290.0864-0.1086-0.02660.2306-0.13330.2890.03290.1242-0.0513-0.430.0801-0.00860.0570.48440.05570.29070.07340.15090.43090.05490.408160.35247.4471102.8595
300.34440.30030.00510.30640.18970.56980.10220.18740.2610.1413-0.04810.21310.06560.0930.02390.22960.01430.04050.22650.03370.3176144.10928.9796112.0136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 484 through 503 )
2X-RAY DIFFRACTION2chain 'A' and (resid 504 through 520 )
3X-RAY DIFFRACTION3chain 'A' and (resid 521 through 537 )
4X-RAY DIFFRACTION4chain 'A' and (resid 538 through 575 )
5X-RAY DIFFRACTION5chain 'B' and (resid 484 through 506 )
6X-RAY DIFFRACTION6chain 'B' and (resid 507 through 552 )
7X-RAY DIFFRACTION7chain 'B' and (resid 553 through 564 )
8X-RAY DIFFRACTION8chain 'B' and (resid 565 through 575 )
9X-RAY DIFFRACTION9chain 'C' and (resid 484 through 503 )
10X-RAY DIFFRACTION10chain 'C' and (resid 504 through 534 )
11X-RAY DIFFRACTION11chain 'C' and (resid 535 through 538 )
12X-RAY DIFFRACTION12chain 'C' and (resid 539 through 548 )
13X-RAY DIFFRACTION13chain 'C' and (resid 549 through 554 )
14X-RAY DIFFRACTION14chain 'C' and (resid 555 through 575 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 41 )
16X-RAY DIFFRACTION16chain 'D' and (resid 42 through 51 )
17X-RAY DIFFRACTION17chain 'D' and (resid 52 through 88 )
18X-RAY DIFFRACTION18chain 'E' and (resid 484 through 500 )
19X-RAY DIFFRACTION19chain 'E' and (resid 501 through 537 )
20X-RAY DIFFRACTION20chain 'E' and (resid 538 through 553 )
21X-RAY DIFFRACTION21chain 'E' and (resid 554 through 575 )
22X-RAY DIFFRACTION22chain 'F' and (resid 484 through 514 )
23X-RAY DIFFRACTION23chain 'F' and (resid 515 through 552 )
24X-RAY DIFFRACTION24chain 'F' and (resid 553 through 575 )
25X-RAY DIFFRACTION25chain 'G' and (resid 484 through 499 )
26X-RAY DIFFRACTION26chain 'G' and (resid 500 through 552 )
27X-RAY DIFFRACTION27chain 'G' and (resid 553 through 575 )
28X-RAY DIFFRACTION28chain 'H' and (resid 2 through 41 )
29X-RAY DIFFRACTION29chain 'H' and (resid 42 through 50 )
30X-RAY DIFFRACTION30chain 'H' and (resid 51 through 88 )

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