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- PDB-1gzc: High-Resolution crystal structure of Erythrina cristagalli lectin... -

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Basic information

Entry
Database: PDB / ID: 1gzc
TitleHigh-Resolution crystal structure of Erythrina cristagalli lectin in complex with lactose
ComponentsERYTHRINA CRISTA-GALLI LECTIN
KeywordsSUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE / SACCHARIDE / PROTEIN-CARBOHYDRATE INTERACTIONS / LACTOSE / GLYCOPROTEIN
Function / homology
Function and homology information


carbohydrate 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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / 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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-lactose / : / Lectin
Similarity search - Component
Biological speciesERYTHRINA CRISTA-GALLI (cockspur coraltree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsSvensson, C. / Krengel, U.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: High-Resolution Crystal Structures of Erythrina Cristagalli Lectin in Complex with Lactose and 2'-Alpha-L-Fucosyllactose and Correlation with Thermodynamic Binding Data
Authors: Svensson, C. / Teneberg, S. / Nilsson, C. / Kjellberg, A. / Schwarz, F. / Sharon, N. / Krengel, U.
History
DepositionMay 17, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _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_label_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ERYTHRINA CRISTA-GALLI LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6874
Polymers26,2491
Non-polymers4373
Water4,792266
1
A: ERYTHRINA CRISTA-GALLI LECTIN
hetero molecules

A: ERYTHRINA CRISTA-GALLI LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3738
Polymers52,4982
Non-polymers8756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1670 Å2
ΔGint-4.8 kcal/mol
Surface area23350 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.800, 81.800, 126.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ERYTHRINA CRISTA-GALLI LECTIN


Mass: 26249.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) ERYTHRINA CRISTA-GALLI (cockspur coraltree)
References: UniProt: P83410*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE CRYSTALLIZED PROTEIN WAS CONFIRMED BY MASS SPECTROMETRY, BUT THERE ARE ...THE SEQUENCE OF THE CRYSTALLIZED PROTEIN WAS CONFIRMED BY MASS SPECTROMETRY, BUT THERE ARE DISCREPANCIES BETWEEN THE SEQUENCE THAT WAS BUILT INTO ELECTRON DENSITY AND THE MASS SPEC. SEQUENCE, WHICH ARE PROBABLY DUE TO PREFERENTIAL CRYSTALLIZATION OF ONE LECTIN ISOFORM. THE DIFFERENCES BETWEEN THE MASS SPEC-CONFIRMED SEQUENCE AND THE SEQUENCE THAT WAS BUILT INTO THE ELECTRON DENSITY ARE: RES.NUM MS BUILT A 59 ILE MET A 62 MET SER (MAY BE DUE TO CRYSTAL DISORDER)

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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: 4 Å3/Da / Density % sol: 69 %
Description: THE DATA SET INCLUDED REFLECTIONS TO 1.45 A RESOLUTION, BUT THE DATA WERE CUT TO 1.58 A RESOLUTION IN THE FINAL REFINEMENT CYCLE DUE TO CONSIDERABLE INCREASE IN R-FACTORS BEYOND THAT RESOLUTION.
Crystal growpH: 7.5
Details: 2M AMMONIUM SULFATE, 0.1M TRIS PH 7.5, 10% GLYCEROL
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 %lactose1drop
220 mMHEPES1drop
3100 mM1dropNaCl
410 mg/mlprotein1drop
52 Mammonium sulfate1reservoir
60.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.03
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.58→49.8 Å / Num. obs: 58614 / % possible obs: 99.5 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.9
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 551905
Reflection shell
*PLUS
% possible obs: 99.4 % / Num. unique obs: 6065 / Num. measured obs: 38515

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AX1

1ax1


Resolution: 1.58→49.9 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: ALTERNATIVE CONFORMATIONS REFINED FOR RESIDUES 9, 10, 12, 95, 159, 173, 180, 234 LACTOSE ARE DEPOSITED: LAT_XPLOR_TOP.TXT LAT_XPLOR_PAR.TXT. INITIAL STAGES OF REFINEMENT WITH SIMULATED ANNEALING.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 -10 %RANDOM
Rwork0.208 ---
obs0.208 58614 99.5 %-
Solvent computationBsol: 51.5279 Å2 / ksol: 0.385527 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.566 Å20 Å20 Å2
2---4.566 Å20 Å2
3---9.133 Å2
Refinement stepCycle: LAST / Resolution: 1.58→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 25 266 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.0161.5
X-RAY DIFFRACTIONc_mcangle_it2.6162
X-RAY DIFFRACTIONc_scbond_it2.9792
X-RAY DIFFRACTIONc_scangle_it3.9752.5
LS refinement shellResolution: 1.58→1.59 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.343 60 -
Rwork0.334 936 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.6 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 1.64 Å

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