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- PDB-1fny: LEGUME LECTIN OF THE BARK OF ROBINIA PSEUDOACACIA. -

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Basic information

Entry
Database: PDB / ID: 1fny
TitleLEGUME LECTIN OF THE BARK OF ROBINIA PSEUDOACACIA.
ComponentsBARK AGGLUTININ I,POLYPEPTIDE A
KeywordsSUGAR BINDING PROTEIN / legume lectin / 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
Bark agglutinin I polypeptide A
Similarity search - Component
Biological speciesRobinia pseudoacacia (black locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 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 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_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: BARK AGGLUTININ I,POLYPEPTIDE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6512
Polymers25,6111
Non-polymers401
Water3,171176
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)102,6038
Polymers102,4424
Non-polymers1604
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
Unit cell
Length a, b, c (Å)64.078, 75.854, 118.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a tetramer constructed from chain A by two crystallographic two-folds.

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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: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2M ammonium sulphate, 30%(w/v) 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9091
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9091 Å / Relative weight: 1
ReflectionResolution: 1.81→15 Å / Num. all: 26646 / Num. obs: 22296 / % possible obs: 87.4 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Redundancy: 3.67 % / Biso Wilson estimate: 13.922 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.45
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.258 / Num. unique all: 1330 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 15 Å / Observed criterion σ(I): 2 / Num. measured all: 97833

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.81→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2644 9.924 %Random
Rwork0.189 ---
all0.191 26646 --
obs0.191 26642 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.81→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 1 176 1969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.422
X-RAY DIFFRACTIONc_torsion_deg26.181
X-RAY DIFFRACTIONc_torsion_impr_deg0.821
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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