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- PDB-1ofs: Pea lectin-sucrose complex -

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Basic information

Entry
Database: PDB / ID: 1ofs
TitlePea lectin-sucrose complex
Components
  • PEA LECTIN ALPHA CHAIN
  • PEA LECTIN BETA CHAIN
KeywordsLECTIN / PLANT LECTIN / CARBOHYDRATE BINDING PROTEIN / CALCIUM / GLYCOPROTEIN
Function / homology
Function and homology information


D-mannose 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 / Jelly Rolls ...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
sucrose / : / Lectin
Similarity search - Component
Biological speciesPISUM SATIVUM (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShevtsov, M.B. / Tsygannik, I.N.
CitationJournal: To be Published
Title: Pea Lectin-Sucrose Complex
Authors: Shevtsov, M.B. / Tsygannik, I.N.
History
DepositionApr 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _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 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: PEA LECTIN ALPHA CHAIN
B: PEA LECTIN BETA CHAIN
C: PEA LECTIN ALPHA CHAIN
D: PEA LECTIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,74810
Polymers51,8734
Non-polymers8756
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.831, 60.803, 136.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2given(1), (1), (1)
DetailsTHE PEA LECTIN MOLECULE NORMALLY EXISTS AS A DIMER. THETWO MONOMERS ARE RELATED BY A PSUEDO TWOFOLD AXIS. EACHMONOMER CONSISTS OF TWO SEPARATE POLYPEPTIDE CHAINS, ALPHAAND BETA. THE ALPHA CHAIN CONSISTS OF 181 RESIDUES AND THEBETA CHAIN CONSISTS OF 52 RESIDUES. THE ALPHA AND BETACHAINS OF MONOMER 1 HAVE BEEN ASSIGNED CHAIN IDENTIFIERS*A* AND *B*, RESPECTIVELY, IN THIS ENTRY. THE ALPHA ANDBETA CHAINS OF MONOMER 2 HAVE BEEN ASSIGNED CHAINIDENTIFIERS *C* AND *D*, RESPECTIVELY, IN THIS ENTRY.THISNUMBERING SCHEME IS DIFFERENT FROM THAT IN THE EARLIERPUBLICATIONS.

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ACBD

#1: Protein PEA LECTIN ALPHA CHAIN


Mass: 20702.758 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-217 / Source method: isolated from a natural source
Details: SUCROSE LIGAND IS PRESENT IN TWO BINDING SITES OF PROTEIN MOLECULE
Source: (natural) PISUM SATIVUM (garden pea) / Organ: SEEDSSeed / References: UniProt: P02867
#2: Protein/peptide PEA LECTIN BETA CHAIN


Mass: 5233.750 Da / Num. of mol.: 2 / Fragment: RESIDUES 218-265 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / Organ: SEEDSSeed / References: UniProt: P02867
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 360 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 1.98 Å3/Da / Density % sol: 37.47 %
Crystal growpH: 6.5
Details: 0.1 M MES PH 6.5, 12% (W/V) PEG 20K, 8% (V/V) ETOH, 40 MM SUCROSE; CRYOSOLUTION: 0.1 M MES PH 6.5, 17% PEG 20K, 60% (V/V) ETOH, 25 MM SUCROSE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2002 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 38608 / % possible obs: 98.1 % / Redundancy: 3.57 % / Biso Wilson estimate: 24.04 Å2 / Rmerge(I) obs: 0.48 / Net I/σ(I): 22.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 5.53 / % possible all: 89.4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTN

1ltn


Resolution: 1.8→14.86 Å / SU B: 2.56 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.20657 1872 5 %RANDOM
Rwork0.166 ---
obs0.168 35393 95.19 %-
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 50 356 3980

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