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- PDB-1fnz: A bark lectin from robinia pseudoacacia in complex with N-acetylg... -

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Basic information

Entry
Database: PDB / ID: 1fnz
TitleA bark lectin from robinia pseudoacacia in complex with N-acetylgalactosamine
ComponentsBARK AGGLUTININ I, POLYPEPTIDE A
KeywordsSUGAR BINDING PROTEIN / jelly roll
Function / homology
Function and homology information


carbohydrate 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 / Jelly Rolls ...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
2-acetamido-2-deoxy-alpha-D-galactopyranose / Bark agglutinin I polypeptide A
Similarity search - Component
Biological speciesRobinia pseudoacacia (black locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsRabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J.
Citation
Journal: Proteins / Year: 2001
Title: Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N-acetylgalactosamine
Authors: Rabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: A legume lectin from the bark of Robinia pseudoacacia crystallizes in two crystal forms: preliminary diffraction analyses
Authors: Rabijns, A. / Verboven, C. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J.
History
DepositionAug 24, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2001Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 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

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Assembly

Deposited unit
A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8723
Polymers25,6111
Non-polymers2612
Water2,702150
1
A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules

A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules

A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules

A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,48812
Polymers102,4424
Non-polymers1,0458
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area8360 Å2
ΔGint-73 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.622, 76.231, 118.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BARK AGGLUTININ I, POLYPEPTIDE A / BARK LECTIN


Mass: 25610.604 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-268 / Source method: isolated from a natural source / Source: (natural) Robinia pseudoacacia (black locust) / Tissue: BARK / References: UniProt: Q41159
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO ACID HETEROGENEITY IS PRESENT FOR THIS PROTEIN. AMINO ACIDS DIFFER DEPENDING ON THE PLANT SOURCE.

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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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2M ammonium sulphate, 30% polyethylene glycol 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8
Details: Rabijns, A., (2000) Acta Crystallogr., Sect.D, 56, 1638.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mg/mlprotein1drop
20.1 MTris1drop
30.2 Mammonium sulfate1reservoir
430 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 18204 / Num. obs: 18204 / % possible obs: 77.2 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Redundancy: 2.94 % / Biso Wilson estimate: 21.748 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.87
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.278 / Num. unique all: 893 / % possible all: 96.5
Reflection
*PLUS
Lowest resolution: 20 Å / Observed criterion σ(I): 2 / Num. measured all: 53508

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.05→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1788 9.822 %RANDOM
Rwork0.197 ---
all0.199 18204 --
obs0.199 14502 96.9 %-
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 16 150 1958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.392
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_torsion_deg25.936
X-RAY DIFFRACTIONc_torsion_impr_deg0.808
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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