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- PDB-9j1d: Structure of ConA/PHE-Man -

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Basic information

Entry
Database: PDB / ID: 9j1d
TitleStructure of ConA/PHE-Man
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Complex / Lectin / Ligand
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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsLi, L. / Chen, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of ConA/PHE-Man
Authors: Li, L. / Chen, G.
History
DepositionAug 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2027
Polymers51,2452
Non-polymers9575
Water00
1
A: Concanavalin-A
B: Concanavalin-A
hetero molecules

A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,40314
Polymers102,4904
Non-polymers1,91410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10070 Å2
ΔGint-89 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.430, 141.430, 80.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-A1EAW / ~{N}2,~{N}9-bis[2-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethoxy]ethyl]-1,10-phenanthroline-2,9-dicarboxamide


Mass: 766.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H46N4O16 / Feature type: SUBJECT OF INVESTIGATION
#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
Has ligand of interestY
Has protein modificationN

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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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl pH 8.5, 2.0M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.49→63.25 Å / Num. obs: 10870 / % possible obs: 100 % / Redundancy: 24.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.039 / Rrim(I) all: 0.19 / Χ2: 1 / Net I/σ(I): 17.7 / Num. measured all: 264888
Reflection shellResolution: 3.49→3.58 Å / % possible obs: 99.9 % / Redundancy: 26.2 % / Rmerge(I) obs: 1.069 / Num. measured all: 20492 / Num. unique obs: 782 / CC1/2: 0.88 / Rpim(I) all: 0.212 / Rrim(I) all: 1.09 / Χ2: 0.93 / Net I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
PHENIX(1.18.2-3874-000)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P9W

4p9w


Resolution: 3.49→53.1 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 535 4.94 %
Rwork0.1963 --
obs0.1979 10822 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.49→53.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 58 0 3676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123760
X-RAY DIFFRACTIONf_angle_d1.8335128
X-RAY DIFFRACTIONf_dihedral_angle_d18.039532
X-RAY DIFFRACTIONf_chiral_restr0.075590
X-RAY DIFFRACTIONf_plane_restr0.008655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.840.31061330.2642507X-RAY DIFFRACTION100
3.84-4.40.27511350.22312526X-RAY DIFFRACTION100
4.4-5.540.1931300.17612562X-RAY DIFFRACTION100
5.54-53.10.21031370.17962692X-RAY DIFFRACTION99

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