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- PDB-3m7j: Crystal structure of the bacteriocin LLPA from pseudomonas sp. in... -

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Basic information

Entry
Database: PDB / ID: 3m7j
TitleCrystal structure of the bacteriocin LLPA from pseudomonas sp. in complex with Met-mannose
ComponentsPutidacin L1
KeywordsANTIMICROBIAL PROTEIN / monocot mannose-binding lectin / bacteriocin / LLPA / Pseudomonas / bacterial toxin / SIRAS / protein-sugar complex / mannose
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
methyl alpha-D-mannopyranoside / Lectin-like bacteriocin
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsLoris, R. / Garcia-Pino, A.
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
DepositionMar 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 1, 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)60,3764
Polymers59,9872
Non-polymers3882
Water2,036113
1
A: Putidacin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1882
Polymers29,9941
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putidacin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1882
Polymers29,9941
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.973, 153.201, 33.914
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 / bacteriocin LLPA


Mass: 29993.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: BW11M1 / Gene: llpa / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GEJ9
#2: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside / Methylglucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M imidazole, 1.3M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8073 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 10, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8073 Å / Relative weight: 1
ReflectionResolution: 2.26→19.645 Å / Num. all: 33688 / Num. obs: 33688 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.33 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 7.1
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3360 / Rsym value: 0.542 / % possible all: 100

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Processing

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

3m7h


Resolution: 2.26→19.644 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.847 / SU ML: 1.72 / Cross valid method: THROUGHOUT / σ(F): 0.05 / σ(I): 0 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 2466 7.74 %RANDOM
Rwork0.1748 29414 --
all0.1748 0 --
obs0.1778 31880 85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.697 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 104.43 Å2 / Biso mean: 44.515 Å2 / Biso min: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1-12.113 Å2-0 Å20 Å2
2---12.626 Å2-0 Å2
3---0.513 Å2
Refinement stepCycle: LAST / Resolution: 2.26→19.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 26 113 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044167
X-RAY DIFFRACTIONf_angle_d0.8375709
X-RAY DIFFRACTIONf_dihedral_angle_d14.7691413
X-RAY DIFFRACTIONf_chiral_restr0.056620
X-RAY DIFFRACTIONf_plane_restr0.003749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.30340.29521190.23751472X-RAY DIFFRACTION80
2.3034-2.35040.28661320.24681537X-RAY DIFFRACTION82
2.3504-2.40140.30481420.22591549X-RAY DIFFRACTION81
2.4014-2.45720.26371210.22161526X-RAY DIFFRACTION80
2.4572-2.51850.28671420.21871551X-RAY DIFFRACTION84
2.5185-2.58640.27151120.21111656X-RAY DIFFRACTION86
2.5864-2.66240.23561290.20241598X-RAY DIFFRACTION84
2.6624-2.74810.21231210.20241629X-RAY DIFFRACTION86
2.7481-2.8460.23371480.20611673X-RAY DIFFRACTION86
2.846-2.95960.24331420.19421643X-RAY DIFFRACTION88
2.9596-3.09380.24321430.19341710X-RAY DIFFRACTION88
3.0938-3.25620.20481380.18851654X-RAY DIFFRACTION88
3.2562-3.45920.22511510.16831699X-RAY DIFFRACTION88
3.4592-3.72460.16861460.15121709X-RAY DIFFRACTION88
3.7246-4.09640.17841360.1431679X-RAY DIFFRACTION87
4.0964-4.68210.15891310.11991711X-RAY DIFFRACTION86
4.6821-5.87270.18581530.14951691X-RAY DIFFRACTION85
5.8727-19.6450.19051600.16731727X-RAY DIFFRACTION83
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)
11.77160.99990.41393.08930.72640.69250.2141-0.0741-0.18310.5969-0.1964-0.01460.29260.1322-0.00530.3173-0.01370.01360.18390.07160.184248.52587.21588.6378
2-0.1707-0.4326-0.26871.7455-0.03691.04920.06650.0115-0.0260.0477-0.14070.5007-0.11790.0320.06090.1868-0.04060.00890.2022-0.00810.313438.431530.9802-1.6545
31.7058-0.4527-0.60230.7423-0.15112.14030.12510.3722-0.139-0.14390.28420.26380.012-1.0733-0.35810.16270.04350.01250.70770.25430.3330.0012-16.01424.2702
41.07970.6205-0.09790.9179-0.94180.87780.042-0.04950.1495-0.19110.1023-0.1312-0.114-0.0804-0.07410.25570.04090.0480.2185-0.00470.191527.3234-12.88713.3678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:127)A4 - 127
2X-RAY DIFFRACTION2(chain A and resid 146:275)A146 - 275
3X-RAY DIFFRACTION3(chain B and resid 4:127)B4 - 127
4X-RAY DIFFRACTION4(chain B and resid 146:275)B146 - 275

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