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- PDB-4led: The Crystal Structure of Pyocin L1 bound to D-rhamnose at 2.37 An... -

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Basic information

Entry
Database: PDB / ID: 4led
TitleThe Crystal Structure of Pyocin L1 bound to D-rhamnose at 2.37 Angstroms
ComponentsPyocin L1
KeywordsSUGAR BINDING PROTEIN / Monocot Mannose Binding Protein / Galanthus nivalis agglutinin / Beta Prism / Bacteriocin / Antimicrobial Protein / Extracellular
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
alpha-D-rhamnopyranose / Bacteriocin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsGrinter, R. / Roszak, A.W. / Mccaughey, L. / Cogdell, C.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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyocin L1
B: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1659
Polymers60,0162
Non-polymers1,1497
Water1,51384
1
A: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5004
Polymers30,0081
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6655
Polymers30,0081
Non-polymers6574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.990, 160.650, 150.570
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-403-

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: Sugar
ChemComp-XXR / alpha-D-rhamnopyranose / alpha-D-rhamnose / 6-deoxy-alpha-D-mannopyranose / D-rhamnose / rhamnose / Rhamnose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
DRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-rhamnopyranoseCOMMON NAMEGMML 1.0
a-D-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 550 MME, 20% PEG 20K, 0.03 M CaCl2, 0.03 M MgCl2 0.1 M MOPS/HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9788 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.37→54.93 Å / Num. obs: 26242 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 43.618 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1922 / % possible all: 99.5

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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 4LE7

4le7


Resolution: 2.37→54.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.595 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.362 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25685 1327 5.1 %RANDOM
Rwork0.20887 ---
all0.21128 26215 --
obs0.21128 24888 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.163 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å2-0 Å2
2--2.35 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.37→54.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 77 84 4131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.024216
X-RAY DIFFRACTIONr_bond_other_d0.0020.023929
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9645772
X-RAY DIFFRACTIONr_angle_other_deg0.81339061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2995514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38424.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22415646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1551513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02966
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_it2.2532.9362047
X-RAY DIFFRACTIONr_mcbond_other2.2522.9362046
X-RAY DIFFRACTIONr_mcangle_it3.6074.3982564
X-RAY DIFFRACTIONr_mcangle_other3.6074.3982565
X-RAY DIFFRACTIONr_scbond_it2.2573.1762169
X-RAY DIFFRACTIONr_scbond_other2.2563.1762170
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.524.6813208
X-RAY DIFFRACTIONr_long_range_B_refined6.34924.1084782
X-RAY DIFFRACTIONr_long_range_B_other6.3524.1084782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.373→2.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 96 -
Rwork0.351 1818 -
obs--99.07 %
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)
13.9910.14823.32670.02410.06113.76220.1680.2056-0.2122-0.0108-0.01660.0290.32220.6133-0.15140.06530.07150.00350.2235-0.01370.133840.0123.08325.615
21.5358-0.1261.01630.702-0.5463.6899-0.02350.06270.00840.00290.0442-0.0965-0.0438-0.1833-0.02070.0021-0.00530.0010.0828-0.05510.09719.84830.2617.568
34.18273.92010.45066.78933.54475.0389-0.66760.55090.1733-0.40840.63810.15580.9038-0.72730.02950.4991-0.4012-0.01750.52840.00140.1859-9.1753.943-18.97
41.84570.9838-0.13312.68120.07872.16340.13580.2687-0.1942-0.1279-0.0084-0.00210.14960.0946-0.12750.0740.0731-0.03590.1667-0.13190.128610.74923.011-11.363
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 - 253
6X-RAY DIFFRACTION4B116 - 227

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