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- PDB-6cxb: Structure of N-truncated R1-type pyocin tail fiber at 1.7 angstro... -

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Basic information

Entry
Database: PDB / ID: 6cxb
TitleStructure of N-truncated R1-type pyocin tail fiber at 1.7 angstrom resolution
ComponentsR1-type pyocin tail fiber protein
KeywordsVIRAL PROTEIN / adhesin / tail fiber / fiber / phage / pyocin / R2-type / tailocin / carbohydrate binding
Function / homologyPhage tail fibre protein / Phage tail-collar fibre protein / Putative bacteriophage protein
Function and homology information
Biological speciesPseudomonas aeruginosa LESB58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.701 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
DepositionApr 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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 / database_2 / pdbx_initial_refinement_model / 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_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.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_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_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

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Assembly

Deposited unit
A: R1-type pyocin tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5313
Polymers15,4141
Non-polymers1162
Water2,756153
1
A: R1-type pyocin tail fiber protein
hetero molecules

A: R1-type pyocin tail fiber protein
hetero molecules

A: R1-type pyocin tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5929
Polymers46,2433
Non-polymers3496
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8800 Å2
ΔGint-78 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.179, 102.179, 102.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21A-428-

HOH

31A-439-

HOH

41A-450-

HOH

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Components

#1: Protein R1-type pyocin tail fiber protein


Mass: 15414.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A gift from the lab of Dr. Roger C. Levesque
Source: (gene. exp.) Pseudomonas aeruginosa LESB58 (bacteria)
Gene: PAMH19_0675 / Plasmid: pMCSG11
Details (production host): pMCSG11 with fragement of PALES_06171 (R1-NTF) clones in frame into LIC site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A8RA06
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.88 Å3/Da / Density % sol: 57.35 % / Description: Hexagonal prisms.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown at a 1:1 protein (5 mg/mL) to precipitant (100mM Bicine pH 9.5, 20% PEG2k, 1mM CuSO4) ratio

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 19654 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.025 / Rrim(I) all: 0.077 / Χ2: 0.89 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.7-1.733.60.9199810.520.5360.68399.8
1.73-1.764.50.729860.6870.3730.5731000.814
1.76-1.795.30.5579480.8660.260.5981000.616
1.79-1.836.20.5379600.8820.230.6241000.585
1.83-1.877.10.4619690.9240.1830.6741000.497
1.87-1.918.40.4779660.9260.1741.031000.508
1.91-1.9610.60.3829970.9660.1241.0431000.402
1.96-2.0211.10.2349780.9870.0730.781000.245
2.02-2.0710.90.2359690.9870.0751.1521000.246
2.07-2.1411.10.1589710.9930.050.8811000.166
2.14-2.2211.10.139800.9940.0410.7961000.136
2.22-2.3110.90.1589730.9890.0511.2791000.166
2.31-2.4111.10.19920.9960.0310.7561000.105
2.41-2.5411.20.0829810.9960.0260.7991000.086
2.54-2.7110.0749790.9960.0230.881000.078
2.7-2.9111.10.0549840.9970.0170.7311000.057
2.91-3.211.10.0469910.9980.0140.7921000.048
3.2-3.6610.90.0519970.9980.0161.2461000.053
3.66-4.6110.70.0489990.9980.0151.3731000.05
4.61-5010.50.02610530.9990.0080.4331000.027

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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: MOLECULAR REPLACEMENT
Starting model: 6CT8

6ct8


Resolution: 1.701→41.714 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.54
RfactorNum. reflection% reflection
Rfree0.1766 1957 10.04 %
Rwork0.1593 --
obs0.1611 19486 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.85 Å2 / Biso mean: 17.2946 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 1.701→41.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 7 153 1050
Biso mean--17.84 27.67 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005914
X-RAY DIFFRACTIONf_angle_d0.7881251
X-RAY DIFFRACTIONf_chiral_restr0.061147
X-RAY DIFFRACTIONf_plane_restr0.006161
X-RAY DIFFRACTIONf_dihedral_angle_d12.286310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7006-1.74320.24871260.22381100122689
1.7432-1.79030.19461360.18121245138199
1.7903-1.8430.18351410.167312821423100
1.843-1.90250.18071390.172112261365100
1.9025-1.97040.19381390.17712721411100
1.9704-2.04930.1891340.148112341368100
2.0493-2.14260.16931440.144912411385100
2.1426-2.25560.16421400.146512701410100
2.2556-2.39690.20611380.164712501388100
2.3969-2.58190.16761450.16212501395100
2.5819-2.84170.19251400.16512801420100
2.8417-3.25270.16751380.161812601398100
3.2527-4.09750.17051420.138612961438100
4.0975-41.72690.15571550.161713231478100

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