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- PDB-1len: REFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 1len
TitleREFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS RESOLUTION
Components(LECTIN) x 2
KeywordsLECTIN
Function / homology
Function and homology information


carbohydrate mediated signaling / D-mannose binding / manganese ion binding / carbohydrate binding / calcium 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 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
: / PHOSPHATE ION / Lectin
Similarity search - Component
Biological speciesLens culinaris (lentil)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsVan Overberge, D. / Loris, R. / Wyns, L.
Citation
Journal: Proteins / Year: 1994
Title: Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution.
Authors: Loris, R. / Van Overberge, D. / Dao-Thi, M.H. / Poortmans, F. / Maene, N. / Wyns, L.
#1: Journal: Biochemistry / Year: 1993
Title: Crystal Structure Determination and Refinement at 2.3 Angstroms Resolution of the Lentil Lectin
Authors: Loris, R. / Steyaert, J. / Maes, D. / Lisgarten, J. / Pickersgill, R. / Wyns, L.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Two Crystal Forms of the Lentil Lectin Diffract to High Resolution
Authors: Loris, R. / Lisgarten, J. / Maes, D. / Pickersgill, R. / Korber, F. / Reynolds, C. / Wyns, L.
History
DepositionNov 17, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Sep 9, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._citation.title / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,62310
Polymers51,2434
Non-polymers3806
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17800 Å2
ΔGint-137 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.490, 56.370, 82.730
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ALA A 80 - ASP A 81 OMEGA =356.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 80 - ASP C 81 OMEGA =358.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein LECTIN


Mass: 19906.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lens culinaris (lentil) / References: UniProt: P02870
#2: Protein LECTIN


Mass: 5714.288 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lens culinaris (lentil) / References: UniProt: P02870

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Non-polymers , 4 types, 237 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#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


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsEACH MONOMER HAS A BOUND CALCIUM, MANGANESE AMD PHOSPHATE ION. THE CALCIUM AND MANGANESE IONS ARE ...EACH MONOMER HAS A BOUND CALCIUM, MANGANESE AMD PHOSPHATE ION. THE CALCIUM AND MANGANESE IONS ARE ESSENTIAL FOR STABILIZING AN UNUSUAL ALA-ASP CIS PEPTIDE BOND, THAT IS AN ESSENTIAL FEATURE OF THE CARBOHYDRATE RECOGNITION SITE OF THIS LECTIN. THE PHOSPHATE IS BOUND IN THE CARBOHYDRATE RECOGNITION SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal grow
*PLUS
pH: 6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein11
220 mMphosphate11
320 mMacetate11pH6.0
435-40 %(v/v)MPD11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.75 Å / Num. obs: 53882 / % possible obs: 83.7 % / Num. measured all: 169906 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 74.2 % / Rmerge(I) obs: 0.269

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.175 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 14 231 3820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_deg7
Refinement
*PLUS
Rfactor obs: 0.175 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg3
X-RAY DIFFRACTIONp_plane_restr0.013

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