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- PDB-6cu2: Structure of N-truncated R2-type pyocin tail fiber at 2.6 angstro... -

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Basic information

Entry
Database: PDB / ID: 6cu2
TitleStructure 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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 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 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R2-type pyocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4733
Polymers29,3901
Non-polymers832
Water2,936163
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)88,4209
Polymers88,1713
Non-polymers2496
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area21710 Å2
ΔGint-190 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.865, 59.865, 398.049
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-702-

NI

21A-836-

HOH

31A-840-

HOH

41A-853-

HOH

51A-900-

HOH

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Components

#1: Protein R2-type pyocin


Mass: 29390.268 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: pMCSG11
Details (production host): PA0620 cloned in frame into LIC site by ligation independent cloning
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XD71
#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.5 Å3/Da / Density % sol: 64.89 % / Description: Hexagonal prism
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1:1 ratio of protein to precipitant (100mM HEPES pH 8.0, 1M Sodium acetate, 0.4mM LDAO)

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 14554 / % possible obs: 99.8 % / Redundancy: 29.8 % / Biso Wilson estimate: 37.65 Å2 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.041 / Rrim(I) all: 0.24 / Χ2: 2.165 / Net I/σ(I): 5.5 / Num. measured all: 433942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.58-2.62100.7836600.7720.2530.8250.73996.5
2.62-2.6711.60.7386850.8140.2190.7720.78199.3
2.67-2.7213.80.6467360.9110.1780.6710.81699.6
2.72-2.78160.6136680.920.1550.6340.90299.9
2.78-2.8419.30.5587130.9320.1290.5741.009100
2.84-2.9122.10.5016830.9920.1080.5131.17100
2.91-2.9827.20.457240.9720.0870.4591.32100
2.98-3.0634.40.4296970.9790.0730.4351.523100
3.06-3.1539.40.387160.9870.0610.3851.848100
3.15-3.2538.20.3557010.9890.0580.362.005100
3.25-3.3738.20.3147200.9890.0510.3182.381100
3.37-3.5380.2777220.9910.0450.2812.634100
3.5-3.6637.60.2627100.9920.0430.2662.718100
3.66-3.85370.247280.9950.0390.2432.824100
3.85-4.0936.40.2127220.9960.0350.2153.013100
4.09-4.4135.60.1877450.9970.0320.193.25999.9
4.41-4.8535.50.1797470.9960.030.1812.87100
4.85-5.5635.60.1737660.9960.0290.1762.536100
5.56-735.10.1677920.9960.0290.172.106100
7-5030.60.1289190.9980.0240.131.83699.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.92 Å39.8 Å
Translation6.92 Å39.8 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: 2.58→39.805 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2287 1445 10 %
Rwork0.194 --
obs0.1974 14443 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.28 Å2 / Biso mean: 32.6714 Å2 / Biso min: 15.56 Å2
Refinement stepCycle: final / Resolution: 2.58→39.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 2 163 2053
Biso mean--71.82 35.78 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091953
X-RAY DIFFRACTIONf_angle_d0.852671
X-RAY DIFFRACTIONf_chiral_restr0.053272
X-RAY DIFFRACTIONf_plane_restr0.005351
X-RAY DIFFRACTIONf_dihedral_angle_d12.431084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5785-2.67070.29341310.26611186131795
2.6707-2.77760.27871420.24812681410100
2.7776-2.90390.29511380.241212511389100
2.9039-3.0570.28091430.237712781421100
3.057-3.24840.26351420.203812711413100
3.2484-3.49910.26771430.19771281142499
3.4991-3.8510.24731450.189912931438100
3.851-4.40760.17581460.160313201466100
4.4076-5.55070.16361490.149313491498100
5.5507-39.80960.20981660.19551501166799

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