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- PDB-1jn2: Crystal Structure of meso-tetrasulphonatophenyl porphyrin complex... -

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Basic information

Entry
Database: PDB / ID: 1jn2
TitleCrystal Structure of meso-tetrasulphonatophenyl porphyrin complexed with Concanavalin A
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / LECTIN
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / 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
: / Chem-SFP / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoel, M. / Jain, D. / Kaur, K.J. / Kenoth, R. / Maiya, B.G. / Swamy, M.J. / Salunke, D.M.
CitationJournal: J.Biol.Chem. / Year: 2000
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 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _struct.pdbx_descriptor / _struct_ref_seq.ref_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE MODEL USED WAS 5CNA WHICH HAS THE SAME SEQUENCE AS THIS STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6564
Polymers25,6221
Non-polymers1,0343
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Concanavalin-A
hetero molecules

P: Concanavalin-A
hetero molecules

P: Concanavalin-A
hetero molecules

P: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,62616
Polymers102,4904
Non-polymers4,13612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area11490 Å2
ΔGint-119 kcal/mol
Surface area34620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.00, 117.3, 126.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 1 / Fragment: UNP P02866 residues 164-281, 30-148 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SFP / 5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE


Mass: 939.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H34N4O12S4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
21.25 Mammonium sulfate1reservoir
30.75 M1reservoirNaCl
41 mMMn2+1reservoir
51 mMCa2+1reservoir
610 mMTris1reservoirpH7.4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 31014 / % possible obs: 94 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.97 Å / % possible all: 88.4
Reflection
*PLUS
Redundancy: 3 % / Num. measured all: 97008
Reflection shell
*PLUS
% possible obs: 88.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→100 Å / Details: THE ASU CONTAINS A HALF OF THE PORPHYRIN LIGAND
RfactorNum. reflectionSelection details
Rfree0.232 3101 Random
Rwork0.195 --
all-97008 -
obs-31014 -
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 35 51 1895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2

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