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- PDB-6ct8: Selenomethionine structure of N-truncated R2-type pyocin tail fib... -

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Basic information

Entry
Database: PDB / ID: 6ct8
TitleSelenomethionine structure of N-truncated R2-type pyocin tail fiber at 2.6 angstrom resolution
ComponentsR2-type pyocin
KeywordsVIRAL PROTEIN / adhesin / tail fiber / fiber / phage / pyocin / R2-type / tailocin / carbohydrate binding
Function / homologyPhage tail fibre protein / : / Phage tail-collar fibre protein, N-terminal / Putative tail fiber protein gp53-like, C-terminal / : / metal ion binding / NICKEL (II) ION / Probable bacteriophage protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.62 Å
AuthorsSalazar, A.J. / Sherekar, M. / Saccettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationA-0015 United States
CitationJournal: PLoS ONE / Year: 2019
Title: R pyocin tail fiber structure reveals a receptor-binding domain with a lectin fold.
Authors: Salazar, A.J. / Sherekar, M. / Tsai, J. / Sacchettini, J.C.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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: R2-type pyocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5902
Polymers29,5311
Non-polymers591
Water1,65792
1
A: R2-type pyocin
hetero molecules

A: R2-type pyocin
hetero molecules

A: R2-type pyocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7696
Polymers88,5933
Non-polymers1763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)59.930, 59.930, 396.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-701-

NI

21A-849-

HOH

31A-854-

HOH

41A-867-

HOH

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Components

#1: Protein R2-type pyocin


Mass: 29530.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0620 / Plasmid: pMCSG-11
Details (production host): contains PA0620 cloned in frame to LIC sites by ligation independent cloning.
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XD71
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.48 Å3/Da / Density % sol: 64.67 % / Description: Hexagonal prisms
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystals were obtained at a 1:1 protein (6mg/mL) to precipitant (1M Na Acetate, 100mM CAPS, 100 mM LiOAc)

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 13424 / % possible obs: 96.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 24.81 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.021 / Rrim(I) all: 0.064 / Χ2: 2.241 / Net I/σ(I): 17.8 / Num. measured all: 103793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.6760.1176330.9930.0490.1281.55897.1
2.67-2.716.50.1156600.9920.0450.1241.50897.9
2.71-2.7780.1126480.9950.0380.121.69699.2
2.77-2.828.60.1086660.9930.0350.1141.83899
2.82-2.888.20.096730.9960.0290.0951.92599.7
2.88-2.958.60.0896440.4510.0350.0981.86199.7
2.95-3.028.40.0776620.9980.0250.0811.75596.1
3.02-3.118.30.076530.9980.0230.0751.82298.3
3.11-3.28.30.076430.9970.0230.0741.93995.7
3.2-3.38.40.0636450.9980.0210.0671.8892.8
3.3-3.428.10.0596300.9970.020.0632.02394.5
3.42-3.567.80.0556390.9980.0180.0582.34292.7
3.56-3.727.50.066660.9950.0210.0642.82295.3
3.72-3.917.80.0586210.9960.0210.0622.87792.5
3.91-4.1670.0546620.9980.020.0582.77793.5
4.16-4.486.70.0456660.9990.0170.0492.47395.1
4.48-4.936.40.0457010.9980.0170.0482.45395.9
4.93-5.647.70.0577020.9980.020.0613.30198.3
5.64-7.118.70.0527500.9970.0180.0562.8299.1
7.11-507.70.0418600.9990.0150.0442.83297.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å41.71 Å
Translation2.5 Å41.71 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.62→45.983 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 2266 10.08 %
Rwork0.1793 20225 -
obs0.1849 22491 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.05 Å2 / Biso mean: 21.3391 Å2 / Biso min: 6.54 Å2
Refinement stepCycle: final / Resolution: 2.62→45.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 1 92 1981
Biso mean--98.05 22.31 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071953
X-RAY DIFFRACTIONf_angle_d0.8512671
X-RAY DIFFRACTIONf_chiral_restr0.051272
X-RAY DIFFRACTIONf_plane_restr0.005351
X-RAY DIFFRACTIONf_dihedral_angle_d17.846648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6201-2.67710.2981370.21471213135092
2.6771-2.73930.35391480.22361354150297
2.7393-2.80780.28281490.20981294144398
2.8078-2.88370.27491540.18791320147498
2.8837-2.96860.30281480.18661303145197
2.9686-3.06440.28511400.19341264140495
3.0644-3.17390.25821420.19131269141192
3.1739-3.30090.22231400.20691212135291
3.3009-3.45110.24511340.19151215134991
3.4511-3.6330.23891320.18061191132389
3.633-3.86050.22741300.17551202133288
3.8605-4.15840.21131360.16531179131588
4.1584-4.57650.18271360.14291250138692
4.5765-5.2380.16091400.14021260140095
5.238-6.59620.20291530.1681353150699
6.5962-45.990.22751470.18551346149399

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