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- PDB-2bqp: THE STRUCTURE OF THE PEA LECTIN-D-GLUCOPYRANOSE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2bqp
TitleTHE STRUCTURE OF THE PEA LECTIN-D-GLUCOPYRANOSE COMPLEX
ComponentsPROTEIN (PEA LECTIN)
KeywordsSUGAR BINDING PROTEIN / PEA LECTIN / D-GLUCOPYRANOSE COMPLEX
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-glucopyranose / : / Lectin
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRuzeinikov, S.N. / Mikhailova Yu, I. / Tsygannik, I.N. / Pangborn, W. / Duax, W. / Pletnev, V.Z.
Citation
Journal: RUSS.J.BIOORGANIC CHEM. / Year: 1997
Title: The Structure of Pea Lectin-D-Glucopyranose Complex at a 1.9 A Resolution
Authors: Pletnev, V.Z. / Ruzheinikov, S.N. / Tsygannik, I.N. / Mikhailova Yu, I. / Duax, W. / Ghosh, D. / Pangborn, W.
#1: Journal: RUSS.J.BIOORGANIC CHEM. / Year: 1998
Title: The Structure of the Pea Lectin-D-Mannopyranose Complex at a 2.1 A Resolution
Authors: Ruzeinikov, S.N. / Mikhailova Yu, I. / Tsygannik, I.N. / Pangborn, W. / Duax, W. / Pletnev, V.Z.
History
DepositionDec 8, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PEA LECTIN)
B: PROTEIN (PEA LECTIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2738
Polymers51,7232
Non-polymers5506
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.838, 135.246, 54.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (PEA LECTIN)


Mass: 25861.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Organ: SEEDS / References: UniProt: P02867
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsD-GLUCOPYRANOSE WAS MODELLED AS A SUPERPOSITION OF ALPHA AND BETA FORMS. THE TWO ALTERNATIVE SUGAR ...D-GLUCOPYRANOSE WAS MODELLED AS A SUPERPOSITION OF ALPHA AND BETA FORMS. THE TWO ALTERNATIVE SUGAR FORMS WERE MARKED BY ADDING A CODE 'A' OR 'B' RESPECTIVELY TO THE BEGINNING OF ATOMS NAMES.

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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: 2.24 Å3/Da / Density % sol: 45.32 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 26905 / % possible obs: 71.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 1.9→2 Å

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQP

1bqp


Resolution: 1.9→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.188 -10 %RANDOM
Rwork0.161 ---
obs0.161 24700 69.5 %-
Displacement parametersBiso mean: 20.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4356 0 53 237 4646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.57
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3_MOD.CHO

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