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- PDB-1jxn: Crystal Structure of the Lectin I from Ulex europaeus in complex ... -

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Basic information

Entry
Database: PDB / ID: 1jxn
TitleCrystal Structure of the Lectin I from Ulex europaeus in complex with the methyl glycoside of alpha-L-fucose
Componentsanti-H(O) lectin I
KeywordsSUGAR BINDING PROTEIN / legume lectin / fucose-specific lectin / UE-I / UEA-I
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
methyl alpha-L-fucopyranoside / : / Anti-H(O) lectin 1
Similarity search - Component
Biological speciesUlex europaeus (furze)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAudette, G.F. / Olson, D.J.H. / Ross, A.R.S. / Quail, J.W. / Delbaere, L.T.J.
CitationJournal: Can.J.Chem. / Year: 2002
Title: Examination of the Structural Basis for O(H) Blood Group Specificity by Ulex europaeus Lectin I
Authors: Audette, G.F. / Olson, D.J.H. / Ross, A.R.S. / Quail, J.W. / Delbaere, L.T.J.
History
DepositionSep 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / 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_ref_seq_dif / 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_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.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_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_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 1.4Aug 16, 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_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: anti-H(O) lectin I
B: anti-H(O) lectin I
C: anti-H(O) lectin I
D: anti-H(O) lectin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,72917
Polymers106,5184
Non-polymers1,21113
Water4,792266
1
A: anti-H(O) lectin I
B: anti-H(O) lectin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8058
Polymers53,2592
Non-polymers5466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-45 kcal/mol
Surface area19020 Å2
MethodPISA
2
C: anti-H(O) lectin I
D: anti-H(O) lectin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9249
Polymers53,2592
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-48 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.810, 69.000, 119.020
Angle α, β, γ (deg.)90.00, 106.76, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological assembly is a homo-dimer. The deposited structure represents the asymmetric unit in which two dimers are present. The first dimer is comprised of chains A and B, and the second dimer is comprised of chains C and D. A single molecule of the methyl glycoside of alpha-L-fucose is present in the carbohydrate binding site of each subunit.

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
anti-H(O) lectin I / UEA-I


Mass: 26629.494 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Ulex europaeus (furze) / Organ: seeds / References: UniProt: P22972
#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.: 4
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

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Non-polymers , 4 types, 275 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.67 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4
Details: MPD, PEG 550MME, sodium acetate, sodium cacodylate, calcium chloride, manganese chloride, pH 4.0, VAPOR DIFFUSION, HANGING DROP at 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 14, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 44883 / % possible obs: 87.9 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 33.627 Å2 / Rsym value: 0.075 / Net I/σ(I): 14.93
Reflection shellResolution: 2.3→2.32 Å / Mean I/σ(I) obs: 2.62 / Num. unique all: 944 / Rsym value: 0.457 / % possible all: 76.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1FX5

1fx5


Resolution: 2.3→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1419 5 %RANDOM
Rwork0.202 ---
obs0.2021 28417 --
all-44883 --
Displacement parametersBiso mean: 21.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7443 0 56 274 7773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.67
X-RAY DIFFRACTIONx_dihedral_angle_d26.14
X-RAY DIFFRACTIONx_improper_angle_d1.3

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