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- PDB-4le7: The Crystal Structure of Pyocin L1 at 2.09 Angstroms -

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Basic information

Entry
Database: PDB / ID: 4le7
TitleThe Crystal Structure of Pyocin L1 at 2.09 Angstroms
ComponentsPyocin L1
KeywordsSUGAR BINDING PROTEIN / Monocot Mannose Binding Lectin / MMBL / Galanthus nivalis agglutinin / GNA / Beta prism / Bacteriocin / Protein Antimicrobial
Function / homology
Function and homology information


Agglutinin, subunit A - #30 / Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsGrinter, R. / Roszak, A.W. / Mccaughey, L. / Cogdell, R.J. / Walker, D.
CitationJournal: Plos Pathog. / Year: 2014
Title: Lectin-Like Bacteriocins from Pseudomonas spp. Utilise D-Rhamnose Containing Lipopolysaccharide as a Cellular Receptor.
Authors: McCaughey, L.C. / Grinter, R. / Josts, I. / Roszak, A.W. / Walen, K.I. / Cogdell, R.J. / Milner, J. / Evans, T. / Kelly, S. / Tucker, N.P. / Byron, O. / Smith, B. / Walker, D.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Pyocin L1
B: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,72947
Polymers60,0162
Non-polymers2,71345
Water5,909328
1
A: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,81731
Polymers30,0081
Non-polymers1,80930
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,91216
Polymers30,0081
Non-polymers90415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.410, 158.400, 147.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-553-

HOH

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Components

#1: Protein Pyocin L1


Mass: 30008.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: C 1433 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: T2LG16*PLUS
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% v/v ethylene glycol, 10% w/v PEG 8000, 0.03 M CaCl2, 0.03 M MgCl2, 0.1 M Tris/Bicine, , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9762 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2012
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.09→36.39 Å / Num. obs: 37131 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.3
Reflection shellResolution: 2.09→2.14 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MSA

1msa


Resolution: 2.09→36.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.601 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R: 0.194 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1858 5 %RANDOM
Rwork0.17808 ---
all0.18027 ---
obs0.18027 35246 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.172 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å20 Å2-0 Å2
2--1.63 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 171 328 4477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.024252
X-RAY DIFFRACTIONr_bond_other_d0.0020.024059
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9595724
X-RAY DIFFRACTIONr_angle_other_deg0.8739327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3835511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68724.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62615641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3681513
X-RAY DIFFRACTIONr_chiral_restr0.120.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1732.4432041
X-RAY DIFFRACTIONr_mcbond_other2.1632.4412040
X-RAY DIFFRACTIONr_mcangle_it3.2943.6472553
X-RAY DIFFRACTIONr_mcangle_other3.2953.6512554
X-RAY DIFFRACTIONr_scbond_it2.4612.7742211
X-RAY DIFFRACTIONr_scbond_other2.462.7742211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7984.0263172
X-RAY DIFFRACTIONr_long_range_B_refined7.79821.6164881
X-RAY DIFFRACTIONr_long_range_B_other7.63921.0434763
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 136 -
Rwork0.263 2615 -
obs--99.71 %
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)
12.66930.0543-1.44240.25650.22071.92310.07740.08180.1132-0.0306-0.047-0.0595-0.1494-0.0633-0.03030.01380.00430.00140.0410.01440.0343-40.22-23.52125.262
22.09360.2334-1.46490.43040.05492.4973-0.1270.032-0.0685-0.12240.1156-0.00230.15930.37030.01150.05480.01190.01560.1620.03430.0538-20.009-29.9197.284
32.59553.3427-2.16726.1102-2.8152.0994-0.0437-0.02350.08380.06220.06760.03670.06670.1755-0.02390.2216-0.01130.00530.09850.03360.13829.081-3.988-19.353
41.82240.424-0.37092.1222-0.27210.81470.21290.18550.2574-0.0254-0.01520.0258-0.1914-0.0878-0.19770.13970.01370.0550.07750.06740.0853-10.852-22.712-11.688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 115
2X-RAY DIFFRACTION1A228 - 255
3X-RAY DIFFRACTION2A116 - 227
4X-RAY DIFFRACTION3B12 - 115
5X-RAY DIFFRACTION3B228 - 254
6X-RAY DIFFRACTION4B116 - 227

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