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- PDB-5mxe: Photorhabdus asymbiotica lectin (PHL) in free form -

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Basic information

Entry
Database: PDB / ID: 5mxe
TitlePhotorhabdus asymbiotica lectin (PHL) in free form
ComponentsPhotorhabdus asymbiotica lectin PHL
KeywordsSUGAR BINDING PROTEIN / lectin / seven-bladed beta-propeller / hydrolase
Function / homologyRepeat of unknown function (DUF346) / metal ion binding / Bulb-type lectin domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica subsp. asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / 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 1.3Jan 17, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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_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_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)40,58913
Polymers40,2131
Non-polymers37612
Water6,539363
1
A: Photorhabdus asymbiotica lectin PHL
hetero molecules

A: Photorhabdus asymbiotica lectin PHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,17726
Polymers80,4262
Non-polymers75124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5730 Å2
ΔGint-246 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.235, 81.235, 113.441
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-657-

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: Chemical
ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→44.16 Å / Num. obs: 34331 / % possible obs: 98.8 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.237 / Num. unique obs: 4583 / CC1/2: 0.934 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C9O

5c9o


Resolution: 1.9→44.16 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.546 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19101 1702 5 %RANDOM
Rwork0.16638 ---
obs0.1676 32591 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.9→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 12 363 3039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192759
X-RAY DIFFRACTIONr_bond_other_d0.0020.022458
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.8753795
X-RAY DIFFRACTIONr_angle_other_deg0.95335620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6985348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24723.77122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12115380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.281515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02703
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_it0.6491.1821386
X-RAY DIFFRACTIONr_mcbond_other0.651.1821385
X-RAY DIFFRACTIONr_mcangle_it1.1261.7691733
X-RAY DIFFRACTIONr_mcangle_other1.1251.7691734
X-RAY DIFFRACTIONr_scbond_it0.7091.2221372
X-RAY DIFFRACTIONr_scbond_other0.7091.2221372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.171.8132061
X-RAY DIFFRACTIONr_long_range_B_refined3.90810.7153639
X-RAY DIFFRACTIONr_long_range_B_other3.24210.1863426
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
Rfree0.236 101 -
Rwork0.217 2112 -
obs--88.31 %

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