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- PDB-1pxd: Crystal structure of the complex of jacalin with meso-tetrasulpho... -

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Basic information

Entry
Database: PDB / ID: 1pxd
TitleCrystal structure of the complex of jacalin with meso-tetrasulphonatophenylporphyrin.
Components
  • Agglutinin alpha chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / lectin / porphyrin
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-SFP / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (chempedak)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoel, M. / Anuradha, P. / Kaur, K.J. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction.
Authors: Goel, M. / Anuradha, P. / Kaur, K.J. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Functional equality in the absence of structural similarity: an added dimension to molecular mimicry
Authors: Goel, M. / Jain, D. / Kaur, K.J. / Kenoth, R. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M.
History
DepositionJul 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6114
Polymers16,7332
Non-polymers1,8782
Water1,02757
1
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,44316
Polymers66,9318
Non-polymers7,5128
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area17980 Å2
ΔGint-85 kcal/mol
Surface area27440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.072, 101.890, 107.657
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 Agglutinin alpha chain / Jacalin alpha chain


Mass: 14673.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / References: UniProt: P18670
#2: Protein/peptide Agglutinin beta-3 chain / Jacalin beta-3 chain


Mass: 2059.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (chempedak) / References: UniProt: P18673
#3: Chemical ChemComp-SFP / 5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE


Mass: 939.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H34N4O12S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.8 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Ammonium sulphate and Sodium chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 2002
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 23948 / Num. obs: 23948 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 10.8 / Num. unique all: 23948 / % possible all: 79.9

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAC

1jac


Resolution: 1.8→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1916 -RANDOM
Rwork0.219 ---
all0.219 19451 --
obs0.219 19451 81.2 %-
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 128 57 1338

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