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- PDB-2ltn: DESIGN, EXPRESSION, AND CRYSTALLIZATION OF RECOMBINANT LECTIN FRO... -

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Basic information

Entry
Database: PDB / ID: 2ltn
TitleDESIGN, EXPRESSION, AND CRYSTALLIZATION OF RECOMBINANT LECTIN FROM THE GARDEN PEA (PISUM SATIVUM)
Components
  • PEA LECTIN, ALPHA CHAIN
  • PEA LECTIN, BETA CHAIN
KeywordsLECTIN
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 ...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
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSuddath, F.L. / Phillips, S.R. / Einspahr, H.
Citation
Journal: J.Biol.Chem. / Year: 1989
Title: Design, expression, and crystallization of recombinant lectin from the garden pea (Pisum sativum).
Authors: Prasthofer, T. / Phillips, S.R. / Suddath, F.L. / Engler, J.A.
#1: Journal: J.Biol.Chem. / Year: 1986
Title: The Crystal Structure of Pea Lectin at 3.0-Angstroms Resolution
Authors: Einspahr, H. / Parks, E.H. / Suguna, K. / Subramanian, E. / Suddath, F.L.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1985
Title: The Location of Manganese and Calcium Ion Cofactors in Pea Lectin Crystals by Use of Anomalous Dispersion and Tuneable Synchrotron X-Radiation
Authors: Einspahr, H. / Suguna, K. / Suddath, F.L. / Ellis, G. / Helliwell, J.R. / Papiz, M.Z.
#3: Journal: J.Biol.Chem. / Year: 1982
Title: The Crystal Structure of Pea Lectin at 6-Angstroms Resolution
Authors: Meehanjunior, E.J. / Mcduffie, J. / Einspahr, H. / Bugg, C.E. / Suddath, F.L.
History
DepositionJun 26, 1990Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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: 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)51,3848
Polymers51,1944
Non-polymers1904
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PEA LECTIN, ALPHA CHAIN
D: PEA LECTIN, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6924
Polymers25,5972
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-60 kcal/mol
Surface area9830 Å2
MethodPISA
3
A: PEA LECTIN, ALPHA CHAIN
B: PEA LECTIN, BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6924
Polymers25,5972
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-61 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.730, 61.160, 136.590
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.

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Components

#1: Protein PEA LECTIN, ALPHA CHAIN


Mass: 20001.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Production host: Escherichia coli (E. coli) / References: UniProt: P02867
#2: Protein PEA LECTIN, BETA CHAIN


Mass: 5596.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / References: UniProt: P02867
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22 %(w/v)PEG33501drop
320 mMsodium cacodylate1drop
420 mMsodium cacodylate1reservoir
540 %(w/v)PEG33501reservoir

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Data collection

Reflection
*PLUS

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.177 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 4 294 3866
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0270.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0140.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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