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- PDB-1fx5: CRYSTAL STRUCTURE ANALYSIS OF ULEX EUROPAEUS LECTIN I -

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Basic information

Entry
Database: PDB / ID: 1fx5
TitleCRYSTAL STRUCTURE ANALYSIS OF ULEX EUROPAEUS LECTIN I
ComponentsANTI-H(O) LECTIN I
KeywordsSUGAR BINDING PROTEIN / Legume lectin / UE-I / homo-dimer / fucose specific lectin
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Anti-H(O) lectin 1
Similarity search - Component
Biological speciesUlex europaeus (furze)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAudette, G.F. / Vandonselaar, M. / Delbaere, L.T.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The 2.2 A resolution structure of the O(H) blood-group-specific lectin I from Ulex europaeus.
Authors: Audette, G.F. / Vandonselaar, M. / Delbaere, L.T.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: 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_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTI-H(O) LECTIN I
B: ANTI-H(O) LECTIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,01811
Polymers53,2592
Non-polymers2,7599
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.610, 70.670, 122.150
Angle α, β, γ (deg.)90.00, 108.60, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9953, 0.09681, 0.00399), (0.09463, 0.96243, 0.2545), (0.0208, 0.25368, -0.96707)
Vector: 24.86527, -8.49005, 56.74289)
DetailsBiological assembly is a homo-dimer. The deposited structure differs from other legume lectins with the presence of a disulfide bond between Cys 115 and Cys 150. The Ala 86 of the Ala-Asp cis-peptide fequently observed in legume lectins is a Thr in UE-I. Residues Glu 28, Lys 83, Asn 240, Thr 241 of chain A and Glu 28, Asn 39, Asn 40, Lys 83, Lys 114, and Asn 240 of chain B were refined as Ala's due to lack of electron density for these side-chains. Several residues differ from the published primary sequence on the basis of the observed electron density. Asn 116 of both chains A and B could not be accomodated in the observed electron density, and was removed; however, residue numbering from 117 to 243 was retained. The final two (2) C-terminal amino acid residues in chain A and final three (3) C-terminal amino acid residues of chain B were not observed in the electron density.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ANTI-H(O) LECTIN I / UEA-I / UE-I


Mass: 26629.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THERE IS AN N-LINKED HEPTASACCHARIDE AT ASN 23 OF CHAIN A AND AN N-LINKED TRISACCHARIDE AT ASN 111 OF CHAINS A AND B
Source: (natural) Ulex europaeus (furze) / Organ: SEEDS / References: UniProt: P22972

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Sugars , 2 types, 3 molecules

#2: Polysaccharide Xylitol-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)- ...Xylitol-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1191.095 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][<C5O4>]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 200 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4
Details: R,S-2-methyl-2,4-pentanediol, sodium acetate, MnCl2, CaCl2, sodium cacodylate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 287.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
20.05 mM1dropCaCl2
30.05 mM1dropMgCl2
422.5 %R,S-MPD1drop
50.05 Msodium acetate1drop
645 %R,S-MPD1reservoir
70.1 Msodium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12871
22871
32871
Diffraction source
SourceTypeIDWavelength
ROTATING ANODEENRAF-NONIUS FR57111.5418
ROTATING ANODEENRAF-NONIUS FR57121.5418
ROTATING ANODEENRAF-NONIUS FR57131.5418
Detector
TypeIDDetectorDate
ENRAF-NONIUS FAST1DIFFRACTOMETERFeb 7, 1994
ENRAF-NONIUS FAST2DIFFRACTOMETERJul 26, 1994
ENRAF-NONIUS FAST3DIFFRACTOMETERMar 28, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 29087 / Num. obs: 29087 / % possible obs: 89.2 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.105 / Num. unique all: 3015 / % possible all: 63.6
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 63.9 %

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Processing

Software
NameVersionClassification
MADNESSdata collection
TRUNCATEdata reduction
AMoREphasing
X-PLOR3.1refinement
MADNESSdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Griffonia simplicifolia lectin IV, 1LEC

1lec


Resolution: 2.2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Simulated Annealing
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2898 10 %RANDOM
Rwork0.171 ---
all0.171 29087 --
obs0.171 29087 89.2 %-
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 176 194 4065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.738
X-RAY DIFFRACTIONx_torsion_deg26.5
X-RAY DIFFRACTIONx_torsion_impr_deg1.527
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. reflection obs: 26189 / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.527

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