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- PDB-6eke: crystal structure of a Pholiota squarrosa lectin unliganded -

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Basic information

Entry
Database: PDB / ID: 6eke
Titlecrystal structure of a Pholiota squarrosa lectin unliganded
Componentslectin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homologymetal ion binding / ACETATE ION / 1,4-BUTANEDIOL / Lectin
Function and homology information
Biological speciesPholiota squarrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsCabanettes, A. / Varrot, A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Recognition of Complex Core-Fucosylated N-Glycans by a Mini Lectin.
Authors: Cabanettes, A. / Perkams, L. / Spies, C. / Unverzagt, C. / Varrot, A.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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.ptnr1_symmetry / _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_label_seq_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: lectin
C: lectin
B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,87714
Polymers14,1343
Non-polymers74311
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, trimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-175 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.229, 67.670, 30.985
Angle α, β, γ (deg.)90.00, 97.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide lectin


Mass: 4711.271 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pholiota squarrosa (fungus) / Plasmid: pET39a-TEV-PhosL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A3B6UEU4*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.17 Å3/Da / Density % sol: 43.37 % / Description: triangle
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 18% butane1,4diol, 300mM zinc acetate, 100 mM imidazole ph 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→33.83 Å / Num. obs: 12666 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.041 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3 / Num. unique obs: 644 / CC1/2: 0.892 / Rpim(I) all: 0.304 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS20160617data reduction
Aimless0.5.27data scaling
SHELXCD2013phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.396 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21119 661 5.2 %RANDOM
Rwork0.17091 ---
obs0.17298 11985 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å2-0.72 Å2
2--1.54 Å2-0 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.7→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms917 0 33 123 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021011
X-RAY DIFFRACTIONr_bond_other_d0.0060.02869
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9171381
X-RAY DIFFRACTIONr_angle_other_deg0.93232008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22924.25547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09615132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.878153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
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_it1.6832.229489
X-RAY DIFFRACTIONr_mcbond_other1.6722.227488
X-RAY DIFFRACTIONr_mcangle_it2.3893.308605
X-RAY DIFFRACTIONr_mcangle_other2.393.311606
X-RAY DIFFRACTIONr_scbond_it2.9132.574522
X-RAY DIFFRACTIONr_scbond_other2.9132.575522
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0093.717776
X-RAY DIFFRACTIONr_long_range_B_refined5.76126.7321126
X-RAY DIFFRACTIONr_long_range_B_other5.65826.1671105
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 52 -
Rwork0.248 839 -
obs--97.8 %

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