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- PDB-5mxf: Photorhabdus asymbiotica lectin (PHL) in complex with alpha-methy... -

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Basic information

Entry
Database: PDB / ID: 5mxf
TitlePhotorhabdus asymbiotica lectin (PHL) in complex with alpha-methyl fucoside
ComponentsPhotorhabdus asymbiotica lectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / seven-bladed beta-propeller / fucose binding site / hydrolase
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / methyl alpha-L-fucopyranoside / Bulb-type lectin domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica subsp. asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJancarikova, G. / Houser, J. / Demo, G. / Wimmerova, M.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity.
Authors: Jancarikova, G. / Houser, J. / Dobes, P. / Demo, G. / Hyrsl, P. / Wimmerova, M.
History
DepositionJan 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 23, 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: Photorhabdus asymbiotica lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,94515
Polymers40,2131
Non-polymers73214
Water5,459303
1
A: Photorhabdus asymbiotica lectin PHL
hetero molecules

A: Photorhabdus asymbiotica lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,89030
Polymers80,4262
Non-polymers1,46428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7100 Å2
ΔGint-234 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.249, 81.249, 113.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Photorhabdus asymbiotica lectin PHL


Mass: 40213.098 Da / Num. of mol.: 1
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: Sugar ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.7-4.3 M NaCl, 100 mM Hepes pH 7.5

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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: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→44.11 Å / Num. obs: 34705 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 11 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4975 / CC1/2: 0.945 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MXE

5mxe


Resolution: 1.9→44.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.735 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19573 1746 5 %RANDOM
Rwork0.16724 ---
obs0.16871 32917 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.486 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 36 303 3011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192797
X-RAY DIFFRACTIONr_bond_other_d0.0060.022501
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.8863850
X-RAY DIFFRACTIONr_angle_other_deg0.93635724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7425352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85323.77122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89615385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7261515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
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_it1.1242.2511390
X-RAY DIFFRACTIONr_mcbond_other1.1232.2511389
X-RAY DIFFRACTIONr_mcangle_it1.73.3651736
X-RAY DIFFRACTIONr_mcangle_other1.73.3661737
X-RAY DIFFRACTIONr_scbond_it1.3022.3811406
X-RAY DIFFRACTIONr_scbond_other1.3012.3811406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0223.5312110
X-RAY DIFFRACTIONr_long_range_B_refined3.84319.5633507
X-RAY DIFFRACTIONr_long_range_B_other3.42319.1053345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 106 -
Rwork0.199 2399 -
obs--100 %

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