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- PDB-4gc2: Crystal structure of the bacteriocin LLPA from pseudomonas sp. in... -

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Basic information

Entry
Database: PDB / ID: 4gc2
TitleCrystal structure of the bacteriocin LLPA from pseudomonas sp. in complex with GlcNAc beta(1-2)Man alpha(1-3)[GlcNAc beta(1-2)Man alpha(1-6)]Man
ComponentsPutidacin L1
KeywordsANTIMICROBIAL PROTEIN / Monocot-lectin fold / bacteriocin / mannose based carbohydrates
Function / homologyAgglutinin, 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 / Lectin-like bacteriocin
Function and homology information
Biological speciesPseudomonas sp. BW11M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1201 Å
AuthorsGarcia-Pino, A. / Loris, R.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural Determinants for Activity and Specificity of the Bacterial Toxin LlpA.
Authors: Ghequire, M.G. / Garcia-Pino, A. / Lebbe, E.K. / Spaepen, S. / Loris, R. / De Mot, R.
History
DepositionJul 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,8983
Polymers59,9872
Non-polymers9111
Water4,324240
1
A: Putidacin L1


Theoretical massNumber of molelcules
Total (without water)29,9941
Polymers29,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putidacin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9052
Polymers29,9941
Non-polymers9111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.242, 153.031, 33.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putidacin L1


Mass: 29993.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. BW11M1 (bacteria) / Strain: Pseudomonas putida BW11M1 / Gene: llpA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GEJ9
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2-1-2/a3-b1_a6-d1_b2-c1_d2-e1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Rhap]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole pH 6.5, 1.3 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 9, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8081 Å / Relative weight: 1
ReflectionResolution: 2.12→19.9 Å / Num. all: 45329 / Num. obs: 45329 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081
Reflection shellResolution: 2.12→2.17 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M7H

3m7h


Resolution: 2.1201→19.894 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1877 2285 5.04 %
Rwork0.1554 --
obs0.157 45320 99.94 %
all-45320 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1201→19.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 61 240 4405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094290
X-RAY DIFFRACTIONf_angle_d1.1495877
X-RAY DIFFRACTIONf_dihedral_angle_d13.5721446
X-RAY DIFFRACTIONf_chiral_restr0.092652
X-RAY DIFFRACTIONf_plane_restr0.005768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1201-2.16610.24941310.22212597X-RAY DIFFRACTION100
2.1661-2.21640.24571490.2182645X-RAY DIFFRACTION100
2.2164-2.27180.22531300.20542688X-RAY DIFFRACTION100
2.2718-2.33310.23841510.19242598X-RAY DIFFRACTION100
2.3331-2.40170.2461630.19312659X-RAY DIFFRACTION100
2.4017-2.4790.21811350.18632636X-RAY DIFFRACTION100
2.479-2.56750.22551310.19052667X-RAY DIFFRACTION100
2.5675-2.670.21881360.18262667X-RAY DIFFRACTION100
2.67-2.79120.23631510.18562674X-RAY DIFFRACTION100
2.7912-2.9380.20811390.1752661X-RAY DIFFRACTION100
2.938-3.12140.17961480.172726X-RAY DIFFRACTION100
3.1214-3.36130.19121550.15872673X-RAY DIFFRACTION100
3.3613-3.69760.20941250.13542718X-RAY DIFFRACTION100
3.6976-4.22820.15651420.12422764X-RAY DIFFRACTION100
4.2282-5.31030.12481390.11852760X-RAY DIFFRACTION100
5.3103-19.89450.17271600.14652902X-RAY DIFFRACTION99
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)
11.80160.96570.34093.47980.11971.03950.2074-0.1947-0.24690.6093-0.1584-0.14790.32790.1546-0.02910.3561-0.02070.01590.20080.05650.224348.46196.65988.28
20.99380.2553-0.274.46-1.34682.50920.01240.00650.0085-0.0241-0.05110.50070.0243-0.1280.01890.1424-0.02980.01630.1521-0.03860.254439.496230.3073-1.7406
32.6329-0.6934-0.73060.28690.00640.67640.02670.6506-0.0605-0.1280.25350.3648-0.0725-1.2138-0.24750.34970.08240.04461.0950.29830.53430.1784-15.75193.887
43.41530.4635-0.0452.3215-0.7671.37630.0735-0.13670.1813-0.01190.1461-0.0224-0.1829-0.1486-0.18390.28650.05260.03310.20230.0120.14926.5762-13.67132.75
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 275 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 129 )
4X-RAY DIFFRACTION4chain 'B' and (resid 130 through 275 )

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