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- PDB-1rin: X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2... -

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Basic information

Entry
Database: PDB / ID: 1rin
TitleX-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION
Components(PEA LECTIN) x 2
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
alpha-D-mannopyranose / : / Lectin
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRini, J.M. / Hardman, K.D. / Einspahr, H. / Suddath, F.L. / Carver, J.P.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: X-ray crystal structure of a pea lectin-trimannoside complex at 2.6 A resolution.
Authors: Rini, J.M. / Hardman, K.D. / Einspahr, H. / Suddath, F.L. / Carver, J.P.
#1: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Pea Lectin-Methyl 3,6-Di-O(Alpha-D-Mannopyranosyl)-Alpha-D-Mannopyranoside Complex
Authors: Rini, J.M. / Carver, J.P. / Hardman, K.D.
History
DepositionJan 27, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,99610
Polymers50,4464
Non-polymers5506
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: PEA LECTIN
B: PEA LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4985
Polymers25,2232
Non-polymers2753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-54 kcal/mol
Surface area9750 Å2
MethodPISA
3
C: PEA LECTIN
D: PEA LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4985
Polymers25,2232
Non-polymers2753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-55 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.300, 73.400, 108.500
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 BONDS ALA A 80 - ASP A 81 AND ALA C 80 -ASP C 81 ARE IN THE CIS CONFORMATION. THIS FEATURE IS COMMON TO THIS FAMILY OF LECTINS.

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Components

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

#1: Protein PEA LECTIN


Mass: 19887.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / References: UniProt: P02867
#2: Protein/peptide PEA LECTIN


Mass: 5334.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / References: UniProt: P02867
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 91 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


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsELECTRON DENSITY FOR ONE TERMINAL MANNOSE RESIDUE OF THE TRISACCHARIDE IS SEEN IN EACH OF THE ...ELECTRON DENSITY FOR ONE TERMINAL MANNOSE RESIDUE OF THE TRISACCHARIDE IS SEEN IN EACH OF THE BINDING SITES OF THE DIMER. SEE *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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
213 mM1reservoir(Man)3
340 mMTris-HCl1reservoir
48.6 %(w/v)PEG80001reservoir
50.02 %(w/v)1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 17124 / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.183 / Rfactor obs: 0.183 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 28 87 3678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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