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- PDB-5c9o: Crystal structure of recombinant PLL lectin from Photorhabdus lum... -

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Basic information

Entry
Database: PDB / ID: 5c9o
TitleCrystal structure of recombinant PLL lectin from Photorhabdus luminescens at 1.5 A resolution
ComponentsPLL lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / seven-bladed beta-propeller / fucose-specific
Function / homologyProtein of unknown function DUF346 / Repeat of unknown function (DUF346) / metal ion binding / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 3/17
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / Hyrsl, P. / Wimmerova, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation13-25401S Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0068 Czech Republic
SYLICACZ.1.05/1.1.00/02.0068 Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure.
Authors: Kumar, A. / Sykorova, P. / Demo, G. / Dobes, P. / Hyrsl, P. / Wimmerova, M.
History
DepositionJun 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,51118
Polymers41,9451
Non-polymers1,56617
Water7,296405
1
A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules

A: PLL lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,04272
Polymers167,7804
Non-polymers6,26268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area25080 Å2
ΔGint-98 kcal/mol
Surface area44380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.787, 87.825, 158.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-227-

CYS

21A-638-

HOH

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Components

#1: Protein PLL lectin


Mass: 41944.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu0732 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N8J0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density meas: 998259.938 Mg/m3 / Density % sol: 57.78 % / Description: prism
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 2.5 % ethanol, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.5→79.17 Å / Num. obs: 80153 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 28.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C9L

5c9l


Resolution: 1.5→39.17 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.695 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1517 4023 5 %RANDOM
Rwork0.13107 ---
obs0.13208 76120 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0 Å2
2--0.12 Å20 Å2
3----0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.5→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 102 405 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0193023
X-RAY DIFFRACTIONr_bond_other_d0.0030.022746
X-RAY DIFFRACTIONr_angle_refined_deg2.5341.9024144
X-RAY DIFFRACTIONr_angle_other_deg1.27336306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4645388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87524.275131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98715425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2681514
X-RAY DIFFRACTIONr_chiral_restr0.1880.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023450
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02750
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_it1.8371.1261460
X-RAY DIFFRACTIONr_mcbond_other1.7921.1241459
X-RAY DIFFRACTIONr_mcangle_it2.7871.6891833
X-RAY DIFFRACTIONr_mcangle_other2.7891.6911834
X-RAY DIFFRACTIONr_scbond_it2.9671.3221561
X-RAY DIFFRACTIONr_scbond_other2.9521.3231561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.171.8962296
X-RAY DIFFRACTIONr_long_range_B_refined5.92711.1063768
X-RAY DIFFRACTIONr_long_range_B_other5.58810.1093529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.17 305 -
Rwork0.148 5539 -
obs--99.95 %

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