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- PDB-6cl5: Structure of P. aeruginosa R1 pyocin fiber PALES_06171 comprising... -

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Open data


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Basic information

Entry
Database: PDB / ID: 6cl5
TitleStructure of P. aeruginosa R1 pyocin fiber PALES_06171 comprising C-terminal residues 323-701
ComponentsTail fiber protein
KeywordsVIRAL PROTEIN / R-type pyocin / Pseudomonas aeruginosa / contractile injection system / receptor-binding protein
Function / homologyPhage tail fibre protein / Phage tail-collar fibre protein / : / Phage tail protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.324 Å
AuthorsButh, S.A. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
SNSF31003A_127092 Switzerland
EPFL running cost grant577-1 Switzerland
CitationJournal: Viruses / Year: 2018
Title: Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.
Authors: Buth, S.A. / Shneider, M.M. / Scholl, D. / Leiman, P.G.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 4, 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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail fiber protein
B: Tail fiber protein
C: Tail fiber protein
D: Tail fiber protein
E: Tail fiber protein
F: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,77016
Polymers244,4726
Non-polymers29810
Water36,5342028
1
A: Tail fiber protein
B: Tail fiber protein
C: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3858
Polymers122,2363
Non-polymers1495
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33420 Å2
ΔGint-285 kcal/mol
Surface area39890 Å2
MethodPISA
2
D: Tail fiber protein
E: Tail fiber protein
F: Tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3858
Polymers122,2363
Non-polymers1495
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33370 Å2
ΔGint-286 kcal/mol
Surface area39810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.504, 155.031, 200.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tail fiber protein / Tail fiber protein


Mass: 40745.281 Da / Num. of mol.: 6 / Fragment: C-terminal domain (UNP residues 323-701)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: LESB58 / Gene: HR1, CRX60_29890 / Plasmid: pTSL (pET23 derivative)
Details (production host): pET23 with cloned SlyD gene, N-terminal His-tag and a TEV recognition site
Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9KW03
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2028 / 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: 4.59 Å3/Da / Density % sol: 73.22 % / Description: blocks
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 500 mM sodium malonate, 100 mM HEPES, pH 6.0 / PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: vaporized nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 30, 2012 / Details: Dynamically bendable mirror and KB mirror pair
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.324→50 Å / Num. obs: 371962 / % possible obs: 99.2 % / Redundancy: 3.45 % / Biso Wilson estimate: 47 Å2 / Rrim(I) all: 0.105 / Net I/σ(I): 8.8
Reflection shellResolution: 2.324→2.46 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.08 / Num. unique obs: 58288 / Rrim(I) all: 0.614 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(dev_3042: ???)refinement
XDSDecember 31, 2011data reduction
XDSDecember 31, 2011data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CL6
Resolution: 2.324→47.69 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 18500 4.98 %
Rwork0.1688 --
obs0.1706 371336 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.324→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16848 0 10 2028 18886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317328
X-RAY DIFFRACTIONf_angle_d0.623766
X-RAY DIFFRACTIONf_dihedral_angle_d8.639936
X-RAY DIFFRACTIONf_chiral_restr0.0472604
X-RAY DIFFRACTIONf_plane_restr0.0043108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3235-2.34990.32365230.32419853X-RAY DIFFRACTION83
2.3499-2.37760.32216260.296711725X-RAY DIFFRACTION99
2.3776-2.40660.30636230.282111818X-RAY DIFFRACTION100
2.4066-2.4370.3146190.260611843X-RAY DIFFRACTION100
2.437-2.46910.28256200.246811807X-RAY DIFFRACTION100
2.4691-2.50290.28136260.238411856X-RAY DIFFRACTION100
2.5029-2.53870.2926180.227211846X-RAY DIFFRACTION100
2.5387-2.57660.25136270.219411893X-RAY DIFFRACTION100
2.5766-2.61680.27226220.216511792X-RAY DIFFRACTION100
2.6168-2.65970.25746170.210511843X-RAY DIFFRACTION100
2.6597-2.70560.26226150.207511784X-RAY DIFFRACTION100
2.7056-2.75480.24426220.200211869X-RAY DIFFRACTION99
2.7548-2.80780.23326190.190711812X-RAY DIFFRACTION100
2.8078-2.86510.23376230.188111883X-RAY DIFFRACTION100
2.8651-2.92740.25186170.185711833X-RAY DIFFRACTION100
2.9274-2.99540.23316180.177511820X-RAY DIFFRACTION100
2.9954-3.07030.20796240.176511868X-RAY DIFFRACTION100
3.0703-3.15330.22856170.172511857X-RAY DIFFRACTION100
3.1533-3.24610.19426220.159811841X-RAY DIFFRACTION100
3.2461-3.35090.19966250.16811819X-RAY DIFFRACTION99
3.3509-3.47060.19796210.162411802X-RAY DIFFRACTION99
3.4706-3.60950.19726190.154811857X-RAY DIFFRACTION100
3.6095-3.77370.18566200.150811863X-RAY DIFFRACTION100
3.7737-3.97260.18286120.142411814X-RAY DIFFRACTION100
3.9726-4.22130.15716280.130311894X-RAY DIFFRACTION100
4.2213-4.5470.14376190.116611753X-RAY DIFFRACTION99
4.547-5.00420.14976170.109911864X-RAY DIFFRACTION100
5.0042-5.72720.1456300.119911888X-RAY DIFFRACTION100
5.7272-7.21170.20466140.160611791X-RAY DIFFRACTION99
7.2117-47.70.2275970.210411648X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5115-0.16630.11031.1166-0.27440.3149-0.017-0.07130.07240.10170.0139-0.1861-0.07130.0237-0.00030.4411-0.0127-0.01350.36260.02370.61582.965957.58770.9167
21.26820.8230.32580.8353-0.04440.21370.1003-0.1288-0.14740.1003-0.11970.0763-0.0098-0.0519-0.00030.446-0.0205-0.00990.37870.01990.558731.248347.31378.6246
30.41910.43510.20671.11091.0181.1198-0.0933-0.2592-0.1887-0.25430.2518-0.3296-0.33720.0625-0.37010.5208-0.0050.21651.6034-0.27221.4736-36.787148.728923.7593
40.4622-0.10410.1050.439-0.08920.02090.1897-0.083-0.3298-0.1072-0.0560.0117-0.06890.66340.07810.46330.0160.2071.4511-0.08991.0164-59.704846.222827.1364
50.0668-0.0757-0.19030.6111-0.3241.00160.2008-0.22650.178-0.28050.34050.16820.0051-0.03870.03980.4661-0.00610.09650.84010.12750.6675-87.515847.75429.779
60.362-0.56850.18980.9124-0.18941.15210.1206-0.11730.072-0.240.50360.32110.2488-0.37640.79260.57310.03890.10880.85210.2310.6534-93.459745.421931.4855
70.10770.1803-0.01260.80360.15950.88270.0013-0.3088-0.11510.12020.46280.71150.0541-0.29240.33020.52530.10830.13360.89580.23470.5681-96.07747.541835.5979
81.3483-0.3740.3230.83730.09390.2846-0.02250.1159-0.1365-0.16380.0024-0.1580.03830.0099-00.4509-0.0002-0.00660.37650.02120.570880.090147.8192-11.2794
90.15160.138-0.15830.4639-0.02060.1250.0860.35920.1891-0.466-0.1195-0.34090.09450.0434-0.00010.46250.0062-0.03710.358-0.02910.449539.823458.8603-12.5171
100.86440.6717-0.07140.1356-0.16180.4410.05520.13870.0274-0.0595-0.13120.4077-0.157-0.1803-0.08190.39460.0210.00250.3344-0.10850.669119.26952.8912.5761
110.00230.0508-0.0002-0.02710.01780.00770.1982-0.49640.57140.03170.2042-0.306-0.2556-0.14030.49370.3684-0.00050.22852.1443-0.42961.3595-48.422451.837829.5564
120.3821-0.1234-0.46220.30350.18750.7173-0.0844-0.2410.12510.304-0.17220.09080.143-0.0737-0.03170.86240.1299-0.10252.2447-0.28150.6339-74.054245.209349.6955
130.0387-0.13260.07750.5984-0.1160.07440.1893-0.96220.11970.64790.3868-0.2704-0.18770.73140.26350.64960.0930.1271.6345-0.24530.7763-83.660550.046347.8142
140.9919-0.606-0.65270.52920.31610.6408-0.1187-1.02480.33060.47090.60960.015-0.16940.40070.52710.68470.11830.20971.19150.00650.6403-91.662746.916547.5482
150.72540.0053-0.29620.57470.08290.25430.08720.07110.2022-0.1146-0.068-0.1707-0.0799-0.0307-0.00180.46350.0143-0.00570.37790.07040.540974.076163.9213-9.8712
160.5366-0.1350.26320.51680.14710.20970.1034-0.17110.22450.0728-0.12240.2311-0.1453-0.02490.00010.4397-0.01980.04040.349-0.05850.474526.413861.05699.9327
170.15620.0273-0.06030.1895-0.06850.0605-0.0524-0.66230.16530.0648-0.01980.0882-0.036-0.12520.01450.61730.0140.26931.8796-0.30841.3663-35.780747.69826.702
181.03790.0552-1.23030.0026-0.07261.45460.2405-0.48140.360.15580.2059-0.21080.0660.20890.70970.24480.02050.20622.2813-0.11011.0755-50.800744.768235.6907
191.0901-1.0308-0.24071.38710.54610.8895-0.7-1.1193-0.6423-0.27260.7760.33781.30140.7682.27830.63790.23190.16991.10970.3910.6781-85.948132.919539.963
200.00930.0257-0.01770.0854-0.05290.0336-0.08230.0131-0.142-0.08650.09770.25670.11230.025-0.16010.9582-0.31450.18021.22360.77631.3695-108.265634.802239.5662
210.05760.3094-0.02731.90750.02040.0533-0.2542-0.6471-0.0927-0.05280.22340.60761.28910.4192-0.30430.68150.11350.15951.08190.32620.6927-88.754133.896439.0229
220.50480.1627-0.04620.48530.04060.35720.00280.0542-0.0522-0.0453-0.0567-0.5137-0.0354-0.025-0.00490.4612-0.00350.01190.34980.00950.715689.494999.82292.602
230.23450.1978-0.14330.1625-0.0710.0797-0.0029-0.0910.1029-0.25430.0953-0.47210.05340.019400.5098-0.00180.00590.34050.02570.528374.5977100.2656-1.2522
241.00520.15880.10740.66170.11710.14710.06640.11280.3577-0.0069-0.09150.0597-0.0307-0.0405-00.42040.02230.00790.34420.01310.589148.7726106.0689-7.3889
250.3055-0.059-0.43530.36510.22750.66020.1218-0.0002-0.422-0.0194-0.15850.12660.0512-0.2113-00.4448-0.0094-0.06470.4979-0.13890.8492.2307102.3119-10.7439
260.23450.07810.1330.505-0.23960.03340.12670.5335-0.04210.08170.0347-0.30650.12210.0850.04690.4954-0.0119-0.11461.1968-0.27550.7877-47.0662106.6835-26.3483
270.48280.3272-0.63461.1136-0.23090.8082-0.11260.42020.2912-0.00220.34740.4458-0.10250.0884-0.00220.4803-0.0391-0.09590.76640.1210.5631-89.0846108.4829-30.8335
280.1821-0.1282-0.14390.2809-0.10020.2441-0.22770.48580.2087-0.28830.32660.1796-0.1070.03790.03310.4916-0.0556-0.13880.85070.13930.4388-92.9934107.0554-34.6077
291.09520.1227-0.21381.07840.20710.4148-0.0054-0.28380.12020.12150.0132-0.23060.003-0.086500.4103-0.0264-0.01790.3541-0.00020.529681.1132107.840512.4866
300.0917-0.1050.12850.1476-0.10630.13920.0992-0.43450.01730.3142-0.17150.10250.0360.12890.00010.4742-0.04880.01050.4189-0.05010.518742.148697.989213.0597
311.0975-0.6492-0.00040.1797-0.08620.26940.0975-0.19610.06020.0816-0.23050.2230.1793-0.1716-0.20470.4142-0.03450.04540.3578-0.13550.672221.89101.8268-0.926
322.0272-1.11220.96430.6825-0.61660.49370.30450.2713-1.2182-0.14220.4252-0.21210.32730.02750.43170.5328-0.0524-0.03921.4541-0.49120.9302-46.2575102.4142-30.2795
330.36370.16370.37120.0660.12181.1165-0.08260.7028-0.2138-0.63430.6281-0.04120.44950.06811.26410.5201-0.3419-0.29851.8702-0.0010.3317-80.4573106.6629-47.7804
342.17890.12640.42291.0816-0.45780.3999-0.38121.41790.3073-0.69470.94140.1341-0.02040.34152.21990.5869-0.3983-0.40731.70590.09160.3938-89.2013106.9612-47.4303
350.34760.1539-0.23120.0592-0.11910.15-0.41830.7030.2003-0.45160.74020.2567-0.0736-0.2080.27770.2734-0.5403-0.46251.84330.13250.288-87.1999109.1525-48.2036
360.6777-0.1420.21641.1533-0.05880.51670.0267-0.1693-0.33520.1171-0.0471-0.26960.0958-0.0859-0.0020.422-0.0509-0.03450.36630.08270.502279.861392.379214.8321
370.3372-0.0064-0.06960.3246-0.27420.19930.04360.0684-0.06840.0058-0.06680.07450.0502-0.0483-00.44210.0134-0.01150.3618-0.01060.51640.820290.9362-6.8277
380.49370.0593-0.19810.2565-0.3120.39330.01380.8546-0.6683-0.02680.02540.03140.099-0.3386-0.42710.34760.0092-0.0690.9811-0.28150.6537-25.7837106.0765-26.0321
390.95910.6758-0.70571.4023-0.07380.7285-0.08660.6160.4568-0.21610.38930.3894-0.48580.60630.36390.5101-0.2246-0.12011.06220.09430.5997-76.3876120.7591-35.8319
400.12710.5595-0.12072.8789-0.80550.2961-0.7690.76760.7221-0.01960.68450.8033-0.68880.4266-0.56250.6345-0.3121-0.28161.18680.44530.7561-88.2002122.2081-41.2319
410.01870.14670.04231.06210.36620.1099-0.32980.17390.3262-0.25080.21450.6265-0.61650.5034-0.02960.8131-0.2601-0.26641.23130.64741.0891-95.6443123.1682-41.926
420.0789-0.21630.07560.9559-0.34550.1385-0.43760.718-0.2329-0.29310.06820.3035-0.83760.5415-0.23750.6374-0.324-0.23881.04930.27760.7865-83.7768120.3258-39.3144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 328:438)
2X-RAY DIFFRACTION2(chain A and resid 439:561)
3X-RAY DIFFRACTION3(chain A and resid 562:577)
4X-RAY DIFFRACTION4(chain A and resid 578:604)
5X-RAY DIFFRACTION5(chain A and resid 605:634)
6X-RAY DIFFRACTION6(chain A and resid 635:684)
7X-RAY DIFFRACTION7(chain A and resid 685:701)
8X-RAY DIFFRACTION8(chain B and resid 328:439)
9X-RAY DIFFRACTION9(chain B and resid 440:485)
10X-RAY DIFFRACTION10(chain B and resid 486:563)
11X-RAY DIFFRACTION11(chain B and resid 564:601)
12X-RAY DIFFRACTION12(chain B and resid 602:607)
13X-RAY DIFFRACTION13(chain B and resid 608:641)
14X-RAY DIFFRACTION14(chain B and resid 642:701)
15X-RAY DIFFRACTION15(chain C and resid 328:464)
16X-RAY DIFFRACTION16(chain C and resid 465:561)
17X-RAY DIFFRACTION17(chain C and resid 562:577)
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