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- PDB-4gc1: Crystal structure of the bacteriocin LLPA from pseudomonas sp. in... -

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Basic information

Entry
Database: PDB / ID: 4gc1
TitleCrystal structure of the bacteriocin LLPA from pseudomonas sp. in complex with Man alpha(1-2)Man
ComponentsPutidacin L1
KeywordsANTIMICROBIAL PROTEIN / Monocot-lectin fold / bacteriocin / mannose based carhydrates
Function / homology
Function and homology information


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
2alpha-alpha-mannobiose / Lectin-like bacteriocin
Similarity search - Component
Biological speciesPseudomonas sp. BW11M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0801 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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)60,6724
Polymers59,9872
Non-polymers6852
Water4,450247
1
A: Putidacin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3362
Polymers29,9941
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putidacin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3362
Polymers29,9941
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.474, 153.140, 33.956
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 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GEJ9
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 3.24 Å3/Da / Density % sol: 62.03 %
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: 2.08→19.7 Å / Num. all: 48205 / Num. obs: 48078 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.84 / Rsym value: 0.402 / % 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: 2.0801→19.699 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 2433 5.06 %
Rwork0.1579 --
obs0.1601 48061 99.87 %
all-48061 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0801→19.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 46 247 4388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114310
X-RAY DIFFRACTIONf_angle_d1.2565915
X-RAY DIFFRACTIONf_dihedral_angle_d13.6441470
X-RAY DIFFRACTIONf_chiral_restr0.097660
X-RAY DIFFRACTIONf_plane_restr0.006772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0801-2.12250.27921450.23622672X-RAY DIFFRACTION100
2.1225-2.16860.28291390.2262583X-RAY DIFFRACTION100
2.1686-2.21890.29291490.22082644X-RAY DIFFRACTION100
2.2189-2.27430.2821510.21242656X-RAY DIFFRACTION100
2.2743-2.33570.21051280.20532619X-RAY DIFFRACTION100
2.3357-2.40440.25291410.20552681X-RAY DIFFRACTION100
2.4044-2.48180.24471490.19822628X-RAY DIFFRACTION100
2.4818-2.57030.25411400.19052654X-RAY DIFFRACTION100
2.5703-2.6730.22021530.18482642X-RAY DIFFRACTION100
2.673-2.79440.24841480.19012673X-RAY DIFFRACTION100
2.7944-2.94120.22881470.18792653X-RAY DIFFRACTION100
2.9412-3.12480.21511350.18412730X-RAY DIFFRACTION100
3.1248-3.3650.25021470.16382683X-RAY DIFFRACTION100
3.365-3.70160.17311260.14362713X-RAY DIFFRACTION100
3.7016-4.23260.14881380.12422769X-RAY DIFFRACTION100
4.2326-5.31520.14321500.11012737X-RAY DIFFRACTION100
5.3152-19.70020.17721470.13462891X-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)
15.5809-0.19130.58156.4062.80926.86240.14580.5822-0.1679-0.1961-0.1945-0.65570.07220.32050.05260.30540.01590.08040.29350.09870.310453.9019.2841-0.5027
21.50870.03060.17812.1411-1.30442.43840.1804-0.2773-0.16191.2443-0.2226-0.30470.39790.40620.10810.5543-0.0616-0.07230.33320.08680.282753.278312.089415.7756
31.47930.85440.96452.6659-1.54982.68630.0821-0.208-0.49540.622-0.1902-0.11150.6420.28190.10360.670.0430.06750.21820.08150.408947.5325-1.478710.3007
41.67510.65620.04922.20030.95731.53180.1101-0.1511-0.15880.3364-0.08510.20180.26260.0864-0.02940.3929-0.0130.07630.19430.07460.327744.00666.11324.889
50.60550.1191-0.45722.5013-0.26390.9660.0531-0.0582-0.01270.1284-0.07310.3748-0.0232-0.02240.02570.2798-0.03970.0280.2076-0.00960.309242.388632.2465-0.2408
64.1710.89850.11615.5160.71154.38480.00740.26790.0301-0.6003-0.04390.3742-0.273-0.11910.04070.2589-0.0079-0.03150.1450.0220.238440.435237.866-9.4071
71.66350.8946-0.2412.8134-1.07172.45-0.1034-0.08340.05140.1941-0.09690.68630.1533-0.26810.16560.261-0.03920.09740.2036-0.03870.422136.811621.08516.244
81.2967-0.1695-0.35930.0809-0.06850.48230.1130.5632-0.0442-0.15390.2140.24890.031-1.2988-0.08320.24370.08080.09921.21520.28920.41740.3577-15.3924.2632
92.67730.3454-0.13422.1899-0.82521.37980.0938-0.07180.1869-0.06240.1176-0.0606-0.1815-0.175-0.20410.30470.05730.05590.18740.0140.174226.5895-13.40642.7624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 129 )
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 165 )
6X-RAY DIFFRACTION6chain 'A' and (resid 166 through 228 )
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 275 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 129 )
9X-RAY DIFFRACTION9chain 'B' and (resid 130 through 275 )

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