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- PDB-9j1b: Structure of ConA/IMI-Man -

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Basic information

Entry
Database: PDB / ID: 9j1b
TitleStructure of ConA/IMI-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, beta chain, Mn/Ca-binding site / Legume lectin domain / : / 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: 2.48 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/IMI-Man
Authors: Li, L. / Chen, G.
History
DepositionAug 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,1557
Polymers51,2452
Non-polymers9105
Water27015
1
A: Concanavalin-A
B: Concanavalin-A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,30914
Polymers102,4904
Non-polymers1,81910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9380 Å2
ΔGint-106 kcal/mol
Surface area35270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.380, 113.720, 83.710
Angle α, β, γ (deg.)90.00, 127.27, 90.00
Int Tables number5
Space group name H-MC121

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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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-A1EAT / ~{N}-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethyl]-4-[3-[4-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethylcarbamoyl]phenyl]imidazol-3-ium-1-yl]benzamide


Mass: 719.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H43N4O14 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
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: 4.34 Å3/Da / Density % sol: 71.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: buffer: 20 mM HEPES, 5 mM CaCl2, 5 mM MnCl2; pH = 7.2, precipitant: Ammonium phosphate

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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: Jun 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→28.76 Å / Num. obs: 30883 / % possible obs: 99.6 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Χ2: 0.93 / Net I/σ(I): 18
Reflection shellResolution: 2.48→2.54 Å / % possible obs: 96.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.547 / Num. measured all: 9200 / Num. unique obs: 2220 / CC1/2: 0.636 / Rpim(I) all: 0.306 / Rrim(I) all: 0.631 / Χ2: 0.7 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P9W

4p9w


Resolution: 2.48→28.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.094 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22756 1472 4.8 %RANDOM
Rwork0.18754 ---
obs0.18949 28944 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.585 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2--0.08 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.48→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 55 15 3688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173343
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.6535125
X-RAY DIFFRACTIONr_angle_other_deg1.2521.597792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5775472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9123.81168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63415578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5311512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02763
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0985.551894
X-RAY DIFFRACTIONr_mcbond_other5.0975.5491893
X-RAY DIFFRACTIONr_mcangle_it7.5228.3182365
X-RAY DIFFRACTIONr_mcangle_other7.528.3172366
X-RAY DIFFRACTIONr_scbond_it5.5315.9331862
X-RAY DIFFRACTIONr_scbond_other5.5295.9321863
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0398.7132761
X-RAY DIFFRACTIONr_long_range_B_refined10.46862.4663782
X-RAY DIFFRACTIONr_long_range_B_other10.46762.4693780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 96 -
Rwork0.268 2081 -
obs--95.02 %

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