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- PDB-4lea: The Crystal Structure of Pyocin L1 bound to D-mannose at 2.55 Ang... -

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Basic information

Entry
Database: PDB / ID: 4lea
TitleThe Crystal Structure of Pyocin L1 bound to D-mannose at 2.55 Angstroms
ComponentsPyocin L1
KeywordsSUGAR BINDING PROTEIN / Mannose Monocot Binding Protein / MMBL / Galanthus nivalis Agglutinin / Beta Prism / Protein Antibiotic / Extra cellular
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
beta-D-mannopyranose / Bacteriocin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)61,63711
Polymers60,0162
Non-polymers1,6219
Water39622
1
A: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9096
Polymers30,0081
Non-polymers9015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyocin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7295
Polymers30,0081
Non-polymers7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.420, 162.060, 152.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
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: I24 / Wavelength: 0.9762 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2012
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.55→55.53 Å / Num. obs: 22096 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 61.517 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 2.55→2.67 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LE7

4le7


Resolution: 2.55→42.28 Å / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.24776 1130 RANDOM
Rwork0.19449 --
all0.19724 20935 -
obs0.19724 20935 -
Refinement stepCycle: LAST / Resolution: 2.55→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 108 22 4120

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