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- PDB-5mxh: Photorhabdus asymbiotica lectin (PHL) in complex with D-galactose -

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Basic information

Entry
Database: PDB / ID: 5mxh
TitlePhotorhabdus asymbiotica lectin (PHL) in complex with D-galactose
ComponentsPhotorhabdus asymbiotica lectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / seven-bladed beta-propeller / D-galactose binding site / hydrolase
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / beta-D-galactopyranose / Bulb-type lectin domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica subsp. asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 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

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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)40,9209
Polymers40,2131
Non-polymers7078
Water4,882271
1
A: Photorhabdus asymbiotica lectin PHL
hetero molecules

A: Photorhabdus asymbiotica lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,83918
Polymers80,4262
Non-polymers1,41316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5510 Å2
ΔGint-87 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.323, 81.323, 114.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Tuner / References: UniProt: C7BLE4
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
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: 14.3 / Wavelength: 0.895 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: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.95→44.35 Å / Num. obs: 32451 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 18.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4636 / CC1/2: 0.877 / % possible all: 100

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Processing

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

5mxe


Resolution: 1.95→44.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.547 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21719 1655 5.1 %RANDOM
Rwork0.17875 ---
obs0.18075 30740 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å2-0 Å2
3----1.8 Å2
Refinement stepCycle: 1 / Resolution: 1.95→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 41 271 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192825
X-RAY DIFFRACTIONr_bond_other_d0.0020.022509
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9013885
X-RAY DIFFRACTIONr_angle_other_deg0.99835747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.825346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2623.871124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.111515
X-RAY DIFFRACTIONr_chiral_restr0.10.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
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_it1.8282.8321384
X-RAY DIFFRACTIONr_mcbond_other1.8232.8311383
X-RAY DIFFRACTIONr_mcangle_it2.644.2361727
X-RAY DIFFRACTIONr_mcangle_other2.6414.2381728
X-RAY DIFFRACTIONr_scbond_it2.2362.9541440
X-RAY DIFFRACTIONr_scbond_other2.2352.9541440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3014.3822158
X-RAY DIFFRACTIONr_long_range_B_refined4.9824.3213465
X-RAY DIFFRACTIONr_long_range_B_other4.75723.9353350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 142 -
Rwork0.248 2206 -
obs--100 %

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