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- PDB-6f5w: Photorhabdus asymbiotica lectin (PHL) in complex with propargyl-f... -

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Basic information

Entry
Database: PDB / ID: 6f5w
TitlePhotorhabdus asymbiotica lectin (PHL) in complex with propargyl-fucoside
Componentslectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / seven-bladed beta-propeller / fucoside
Function / homology: / PLL-like beta propeller / Repeat of unknown function (DUF346) / metal ion binding / propadienyl 6-deoxy-alpha-L-galactopyranoside / PLL-like beta propeller domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsHouser, J. / Jancarikova, G. / Wimmerova, M. / Csavas, M. / Borbas, A. / Herczeg, M. / Fujdiarova, E. / Kover, E.K.
CitationJournal: Chemistry / Year: 2018
Title: Synthesis of alpha-l-Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus asymbiotica Lectin (PHL).
Authors: Jancarikova, G. / Herczeg, M. / Fujdiarova, E. / Houser, J. / Kover, K.E. / Borbas, A. / Wimmerova, M. / Csavas, M.
History
DepositionDec 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.6Dec 10, 2025Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lectin PHL
B: lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,63838
Polymers80,4262
Non-polymers3,21236
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-190 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.571, 80.571, 224.799
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

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Components

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Protein / Sugars , 2 types, 13 molecules AB

#1: Protein lectin PHL


Mass: 40213.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica (bacteria) / Gene: PAU_00698 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): tuner / References: UniProt: C7BLE4
#5: Sugar
ChemComp-KG1 / propadienyl 6-deoxy-alpha-L-galactopyranoside / propargyl-fucoside / propadienyl 6-deoxy-alpha-L-galactoside / propadienyl 6-deoxy-L-galactoside / propadienyl 6-deoxy-galactoside


Type: L-saccharide / Mass: 202.204 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C9H14O5 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 490 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5M NaCl, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→44.96 Å / Num. obs: 63648 / % possible obs: 99.79 % / Redundancy: 10.9 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.065 / Rrim(I) all: 0.216 / Net I/σ(I): 9.4
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.319 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9584 / CC1/2: 0.662 / Rpim(I) all: 0.428 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.4.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MXE

5mxe


Resolution: 1.91→44.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.65 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21288 3273 4.9 %RANDOM
Rwork0.17282 ---
obs0.17479 63648 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.698 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å2-0 Å2
3----1.68 Å2
Refinement stepCycle: 1 / Resolution: 1.91→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 194 465 5972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195671
X-RAY DIFFRACTIONr_bond_other_d0.0060.025068
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9077793
X-RAY DIFFRACTIONr_angle_other_deg0.955311567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8035692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44823.796245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09115756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.6961530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021435
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_it1.4122.3532759
X-RAY DIFFRACTIONr_mcbond_other1.4112.3522758
X-RAY DIFFRACTIONr_mcangle_it2.1463.5223448
X-RAY DIFFRACTIONr_mcangle_other2.1463.5233449
X-RAY DIFFRACTIONr_scbond_it1.6932.5232912
X-RAY DIFFRACTIONr_scbond_other1.6922.5242913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5873.7214344
X-RAY DIFFRACTIONr_long_range_B_refined4.36820.4826886
X-RAY DIFFRACTIONr_long_range_B_other4.11520.1926717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.906→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 225 -
Rwork0.275 4573 -
obs--98.26 %

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