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- PDB-2lal: CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 2.3 ANGSTROMS R... -

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Basic information

Entry
Database: PDB / ID: 2lal
TitleCRYSTAL STRUCTURE DETERMINATION AND REFINEMENT AT 2.3 ANGSTROMS RESOLUTION OF THE LENTIL LECTIN
Components(LENTIL 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
AuthorsLoris, R. / Steyaert, J. / Maes, D. / Lisgarten, J. / Pickersgill, 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: 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
DepositionJun 10, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LENTIL LECTIN (ALPHA CHAIN)
B: LENTIL LECTIN (BETA CHAIN)
C: LENTIL LECTIN (ALPHA CHAIN)
D: LENTIL LECTIN (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,62310
Polymers51,2434
Non-polymers3806
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18000 Å2
ΔGint-135 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.810, 125.470, 56.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE PEPTIDE BOND BETWEEN ALA A 80 AND ASP A 81 AND THE PEPTIDE BOND BETWEEN ALA C 80 AND ASP C 81 ARE BOTH IN THE CIS CONFORMATION.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999971, 0.004373, -0.006242), (0.004401, -0.99998, 0.004515), (-0.006222, -0.004542, -0.99997)
Vector: 0.05748, 107.62639, 113.39713)

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Components

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LENTIL LECTIN ... , 2 types, 4 molecules ACBD

#1: Protein LENTIL LECTIN (ALPHA CHAIN)


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


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

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Non-polymers , 4 types, 221 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.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound 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. THESE SITES ARE PRESENTED ON *SITE* RECORDS BELOW.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal grow
*PLUS
pH: 6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mllentil lectin11
220 mMphosphate11
320 mMacetate11
435-40 %(v/v)MPD12

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 39656 / % possible obs: 75.5 % / Num. measured all: 108765 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 63.1 % / Rmerge(I) obs: 0.238

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.189 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 14 215 3779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d0.033
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_plane_restr / Dev ideal: 0.013

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