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- PDB-4jiv: VCA0105 PAAR-repeat protein from Vibrio cholerae in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4jiv
TitleVCA0105 PAAR-repeat protein from Vibrio cholerae in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5
Components
  • Putative uncharacterized protein
  • Tail-associated lysozyme
KeywordsHYDROLASE/PROTEIN BINDING / PAAR-repeat motif / membrane piercing / type VI secretion system / Vibrio cholerae VgrG2 / cell puncturing device / beta-helix / T4 gp5 / VgrG tip / T6SS spike / HYDROLASE-PROTEIN BINDING complex
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 / metal ion binding
Similarity search - Function
Tumour Suppressor Smad4 - #60 / 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) / PAAR motif / PAAR motif / Tumour Suppressor Smad4 / T4-type lysozyme ...Tumour Suppressor Smad4 - #60 / 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) / PAAR motif / PAAR motif / Tumour Suppressor Smad4 / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
9-OCTADECENOIC ACID / PALMITIC ACID / STEARIC ACID / Pre-baseplate central spike protein Gp5 / Uncharacterized protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Vibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsButh, S.A. / Leiman, P.G. / Shneider, M.M.
CitationJournal: 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.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail-associated lysozyme
B: Tail-associated lysozyme
C: Tail-associated lysozyme
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5519
Polymers38,6384
Non-polymers9135
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24940 Å2
ΔGint-63 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.703, 113.703, 76.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-765-

HOH

21A-820-

HOH

31B-745-

HOH

41B-759-

HOH

51C-809-

HOH

61C-812-

HOH

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Tail-associated lysozyme / Protein Gp5 / Gp5* / Gp5C


Mass: 9847.715 Da / Num. of mol.: 3 / Fragment: gp5G484, UNP RESIDUES 484-575 / Mutation: T566H, D568V, R571A, D573N, I574L, G575N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 5 / Plasmid: pEEva2, a pET-23a derivative / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P16009, lysozyme
#2: Protein Putative uncharacterized protein / VCA0105


Mass: 9095.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Strain: N16961 / Gene: VC_A0105 / Plasmid: pATE, a pACYCDuet-1 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9KN60

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Non-polymers , 6 types, 458 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-STE / STEARIC ACID


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


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 453 / 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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 13-15% PEG 2000, 100mM NaAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012 / 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: 1.9→80.4 Å / Num. all: 75604 / Num. obs: 75505 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.97
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.85 / Num. unique all: 12269 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→80.4 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 3781 5.01 %RANDOM
Rwork0.1636 ---
all0.1657 75604 --
obs0.1657 75476 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.903→80.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 60 453 3180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073002
X-RAY DIFFRACTIONf_angle_d0.9954108
X-RAY DIFFRACTIONf_dihedral_angle_d13.7091096
X-RAY DIFFRACTIONf_chiral_restr0.076469
X-RAY DIFFRACTIONf_plane_restr0.003548
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9033-1.92740.22881340.2285259497
1.9274-1.95280.21011410.21832672100
1.9528-1.97950.23791410.21722666100
1.9795-2.00780.26841330.20932635100
2.0078-2.03780.23281400.20222659100
2.0378-2.06960.21691380.19482655100
2.0696-2.10360.22731440.20322674100
2.1036-2.13980.27381430.1982665100
2.1398-2.17880.21181400.19392659100
2.1788-2.22070.26671360.17562628100
2.2207-2.2660.19151410.17872669100
2.266-2.31530.19921400.18012676100
2.3153-2.36910.19321370.17562652100
2.3691-2.42840.22041370.17642640100
2.4284-2.49410.23391460.19392659100
2.4941-2.56740.21611410.18182636100
2.5674-2.65030.25171440.18612678100
2.6503-2.74510.25891400.18132669100
2.7451-2.8550.23971370.17652667100
2.855-2.98490.2541440.17842656100
2.9849-3.14230.17731370.16952624100
3.1423-3.33920.20741450.16052686100
3.3392-3.5970.20181400.1372631100
3.597-3.95890.2021460.13262661100
3.9589-4.53180.17321420.13152653100
4.5318-5.70930.16451370.13072674100
5.7093-80.4720.19981370.16892657100
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)
19.68823.4922-2.17667.8547-0.92824.3750.1628-0.18620.5342-0.34330.164-0.2034-0.44190.2879-0.24150.4299-0.02430.0680.3361-0.01940.4678118.688-11.96934.5512
22.06020.6788-1.00891.9189-0.17971.11540.10020.01610.0194-0.42330.00620.4364-0.2118-0.193-0.2330.33560.0789-0.03790.33250.00520.3592104.4216-19.147832.6053
35.17583.3074-5.31693.0021-3.31885.6221-0.19910.48570.0611-0.80940.21050.1390.0901-0.16560.02580.86830.0236-0.03830.30090.08690.3086109.7477-17.299314.6207
42.4704-1.3025-0.58471.0466-0.51352.05420.1341-0.11830.1668-0.29240.1314-0.4785-0.41220.39430.08260.436-0.08330.13690.15860.01480.4218125.2172-19.129623.5421
52.03850.3866-0.63710.74520.16232.3197-0.05850.0490.2202-0.58890.05760.03420.0630.02090.05460.4350.0172-0.0350.22180.03640.2474112.6176-31.079122.9011
60.2778-0.1436-0.05651.0425-0.62041.3979-0.2126-0.0120.0128-0.99510.1417-0.6790.1777-0.03190.0510.5577-0.03070.1550.2678-0.01970.5038126.9685-34.228420.2674
72.20810.1516-0.24393.0122-0.66525.09870.1042-0.0055-0.1515-0.51910.0656-0.27650.0888-0.0033-0.09240.35210.00850.04520.1962-0.00930.2197117.1012-44.894324.7788
81.9597-0.1551-0.76270.0644-0.01790.397-0.03610.2760.0242-0.66310.01-0.19340.0693-0.0387-0.12820.9681-0.00930.22980.2302-0.00920.1937123.4672-44.71459.8497
90.7386-0.2315-0.08190.09520.0290.0154-0.01140.0963-0.0021-1.01140.2276-0.7217-0.17520.206-0.02420.6497-0.02940.25720.2307-0.04210.4265126.146-56.21616.6088
103.48210.52790.06011.9261.8134.6049-0.43580.27280.3959-0.45010.68450.3377-0.3078-0.5321-0.12581.04880.01830.09960.47910.10250.5515115.147-8.712816.8512
113.51460.9014-0.84052.9684-0.21722.91890.3229-0.2067-0.0737-0.0866-0.0345-0.4927-0.41890.3307-0.35370.29890.00740.05820.1956-0.0150.2925116.5295-16.814531.9868
123.27390.5508-2.60090.1048-0.51447.0784-0.06420.35250.2235-0.98750.040.1708-0.4608-0.27080.050.59010.0023-0.08250.25490.05490.2998109.2348-23.330818.49
134.3893-0.52764.26030.77010.19744.93190.10390.46430.5945-0.34970.0497-0.193-0.40430.3958-0.13110.5596-0.05070.14540.28520.02210.424125.2134-22.246919.0157
146.73953.4853-2.74592.5987-1.5851.55360.2294-0.11230.0186-0.25750.075-0.4549-0.05040.1456-0.35650.2802-0.01050.07070.2544-0.01740.3921122.4288-30.820329.5605
152.78380.3693-0.71030.5407-0.59111.4633-0.1144-0.1615-0.0446-0.9355-0.1445-0.07620.02670.1514-0.53780.6717-0.03980.05890.16120.02990.2438117.2159-36.320817.4645
164.08872.9161-1.36042.5838-1.83572.54030.0551-0.374-0.1056-0.3398-0.0083-0.9156-0.12670.2818-0.15510.388-0.01330.16420.2385-0.07330.3992127.0991-42.935924.7068
170.5160.2882-1.42020.5886-0.46244.16790.16190.4350.0578-1.15210.293-0.4219-0.2044-0.30172.29480.8389-0.01150.280.20640.01750.0508120.6625-49.804913.2408
180.7782-0.41420.43930.39730.37482.41020.33780.00350.1351-0.50560.1899-0.8821-0.0890.35180.38070.5732-0.01280.28340.229-0.06710.5129129.6287-57.775418.0233
194.50972.8585-4.15766.9701-1.37465.9530.28960.02540.0392-0.98750.10060.2568-0.5083-0.3932-0.3640.65660.2091-0.21450.48250.03260.7141102.1033-15.722527.9911
201.50730.7405-2.53242.295-0.79984.45990.2290.52010.2413-1.25240.10990.7803-0.9114-0.2015-0.30840.86230.0206-0.01260.32080.13170.4426113.6376-13.209616.7919
210.11420.1718-0.12970.4028-0.38130.40880.058-0.0256-0.0918-0.10360.0081-0.4351-0.16630.1756-0.07570.3206-0.04450.05630.2594-0.00850.3896121.7758-18.643429.7049
222.73590.4629-2.12792.9411-1.97482.690.20690.0072-0.0056-0.65270.10780.4909-0.131-0.3643-0.26950.3356-0.0066-0.04820.22760.02660.2775108.0271-28.379325.5181
230.6613-0.247-0.08750.9349-0.2040.86270.07540.35020.0991-1.09740.0302-0.25510.2020.00160.2040.827-0.01710.12010.18450.05750.3657120.3889-26.71914.0022
245.72054.2655-0.26953.7014-1.00911.29360.05810.35480.4871-0.45450.1402-0.5202-0.49840.3839-0.0660.3324-0.05920.13920.2617-0.00870.4738125.7149-33.20926.6735
250.3074-0.0907-0.31080.3012-0.28451.17550.12720.2539-0.0018-0.97330.0593-0.4395-0.0531-0.1020.03690.6313-0.02250.18540.189-0.02790.3419122.6452-41.968517.8094
261.7391-0.8351-0.03950.65140.02737.1058-0.0204-0.0808-0.0426-0.61410.3297-0.2786-0.19180.4112-0.08430.5971-0.0140.09030.1928-0.03160.3064120.4535-53.165620.0371
270.23370.08280.18760.9201-0.02210.16860.08880.0890.0761-0.74460.1057-0.6737-0.3220.12780.27510.85170.00340.35870.3296-0.04590.5033130.3122-55.95810.9466
281.08670.01150.48870.79960.33781.35560.24090.1679-0.1127-0.40660.1111-0.5824-0.0710.14840.21210.93090.10060.35340.0621-0.19630.4187132.4544-80.17947.8015
292.47870.41991.98250.98251.07272.21060.1931-0.2461-0.1663-0.1704-0.0065-0.1028-0.0525-0.4394-0.06390.70560.00630.15320.2899-0.00910.3991124.489-68.117615.9249
300.5196-0.4857-0.22771.55680.84830.82110.1245-0.11220.1433-0.12710.1392-0.6165-0.03170.2233-0.20860.6260.02250.12750.2668-0.06650.4841133.813-81.346712.4373
311.76721.41581.27582.45682.16741.9278-0.1596-0.13440.20830.38510.218-0.3608-0.43560.06280.12660.5720.02950.01710.3194-0.06450.5248141.441-95.57488.7953
320.3754-0.09230.22750.41670.22650.33220.1659-0.04180.5180.10560.1714-0.5337-0.07890.11450.19880.7299-0.02330.41250.2241-0.20750.9096138.6712-70.944412.5375
330.61610.1890.11490.87230.68860.53250.0828-0.09030.0582-0.27560.2752-0.61750.10970.11060.40780.84330.02540.44730.1537-0.15810.702138.259-73.50319.8806
342.9969-1.08030.66911.71371.42062.2380.53570.35130.1843-0.7406-0.1301-0.32-0.41760.1541-0.0411.14930.06810.33640.3056-0.06240.4318129.7862-68.44855.0238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 483:488)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 489:495)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 496:501)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 502:510)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 511:525)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 526:536)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 537:544)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 545:553)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 554:575)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 483:488)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 489:500)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 501:510)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 511:515)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 516:522)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 523:537)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 538:548)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 549:560)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 561:575)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 483:488)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 489:496)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 497:506)
22X-RAY DIFFRACTION22(CHAIN C AND RESID 507:514)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 515:522)
24X-RAY DIFFRACTION24(CHAIN C AND RESID 523:530)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 531:552)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 553:562)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 563:575)
28X-RAY DIFFRACTION28(CHAIN D AND RESID 2:27)
29X-RAY DIFFRACTION29(CHAIN D AND RESID 28:32)
30X-RAY DIFFRACTION30(CHAIN D AND RESID 33:49)
31X-RAY DIFFRACTION31(CHAIN D AND RESID 50:54)
32X-RAY DIFFRACTION32(CHAIN D AND RESID 55:67)
33X-RAY DIFFRACTION33(CHAIN D AND RESID 68:84)
34X-RAY DIFFRACTION34(CHAIN D AND RESID 85:94)

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