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- PDB-6flu: Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C... -

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Basic information

Entry
Database: PDB / ID: 6flu
TitlePhotorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside
ComponentsPhotorhabdus asymbitoca lectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / seven-bladed beta-propeller / C-fucoside / Methyl 2 / 3-dideoxy-3-C-[(a-L-fucopyranosyl)methyl]-a-D- arabino-hexopyranoside
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / Chem-DTK / Bulb-type lectin domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica subsp. asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHouser, J. / Jancarikova, G. / Wimmerova, M.
CitationJournal: Sci Rep / Year: 2019
Title: Fucosylated inhibitors of recently identified bangle lectin from Photorhabdus asymbiotica.
Authors: Paulikova, G. / Houser, J. / Kasakova, M. / Oroszova, B. / Bertolotti, B. / Parkan, K. / Moravcova, J. / Wimmerova, M.
History
DepositionJan 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,57623
Polymers80,4262
Non-polymers4,15021
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.940, 81.940, 224.645
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-408-

CL

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Components

#1: Protein Photorhabdus asymbitoca lectin PHL


Mass: 40213.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77 / Gene: PAU_00698 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner / References: UniProt: C7BLE4
#2: Chemical
ChemComp-DTK / (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R},6~{S})-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol


Mass: 322.351 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C14H26O8
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.7 M NaCl, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8943 Å / Relative weight: 1
ReflectionResolution: 1.78→44.93 Å / Num. obs: 85234 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.991 / Rmerge(I) obs: 0.242 / Net I/σ(I): 9
Reflection shellResolution: 1.78→1.87 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.325 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 132122 / CC1/2: 0.53 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→44.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.969 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22218 4196 4.9 %RANDOM
Rwork0.18411 ---
obs0.18599 80956 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.78→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 225 700 6257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195806
X-RAY DIFFRACTIONr_bond_other_d0.0020.025031
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9218019
X-RAY DIFFRACTIONr_angle_other_deg1.046311674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.735717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00923.71248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2115775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3051532
X-RAY DIFFRACTIONr_chiral_restr0.1130.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021247
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_it0.8781.1392790
X-RAY DIFFRACTIONr_mcbond_other0.8781.1392789
X-RAY DIFFRACTIONr_mcangle_it1.3281.7053491
X-RAY DIFFRACTIONr_mcangle_other1.3281.7053492
X-RAY DIFFRACTIONr_scbond_it1.1211.2823016
X-RAY DIFFRACTIONr_scbond_other1.1211.2823017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6821.8944515
X-RAY DIFFRACTIONr_long_range_B_refined3.23214.386863
X-RAY DIFFRACTIONr_long_range_B_other3.0414.0956736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.777→1.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 293 -
Rwork0.287 5879 -
obs--99.07 %

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