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- PDB-9j1f: Dimeric Structure of ConA/M2P-Man -

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Basic information

Entry
Database: PDB / ID: 9j1f
TitleDimeric Structure of ConA/M2P-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: 2.17 Å
AuthorsLi, L. / Chen, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Dimeric Structure of ConA/M2P-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
C: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,40314
Polymers102,4904
Non-polymers1,91410
Water1,17165
1
A: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4356
Polymers51,2452
Non-polymers1904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area18960 Å2
MethodPISA
2
B: Concanavalin-A
hetero molecules

C: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9688
Polymers51,2452
Non-polymers1,7246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.216, 79.070, 87.917
Angle α, β, γ (deg.)90.00, 117.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: 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 / 1,6-DI-O-PHOSPHONO-D-MANNITOL


Mass: 766.746 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H46N4O16 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium chloride, 0.1M Phosphate-citrate pH 4.2 10% (w/v) PEG 3000

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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: 2.17→78.2 Å / Num. obs: 52760 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.983 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.084 / Rrim(I) all: 0.161 / Χ2: 0.69 / Net I/σ(I): 4.4 / Num. measured all: 184071
Reflection shellResolution: 2.17→2.28 Å / % possible obs: 99.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.862 / Num. measured all: 22043 / Num. unique obs: 7613 / CC1/2: 0.369 / Rpim(I) all: 0.602 / Rrim(I) all: 1.058 / Χ2: 0.86 / Net I/σ(I) obs: 2.1

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Processing

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

4p9w


Resolution: 2.17→78.2 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.426 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 2477 4.8 %RANDOM
Rwork0.2087 ---
obs0.21093 49425 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.02 Å2
2---0.11 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.17→78.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 116 65 7417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137520
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176692
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.65410256
X-RAY DIFFRACTIONr_angle_other_deg1.2221.59215604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8185944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22823.81336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.739151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6131524
X-RAY DIFFRACTIONr_chiral_restr0.0630.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028428
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021516
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_it2.7512.9413788
X-RAY DIFFRACTIONr_mcbond_other2.752.943787
X-RAY DIFFRACTIONr_mcangle_it4.6944.4014730
X-RAY DIFFRACTIONr_mcangle_other4.6944.4024731
X-RAY DIFFRACTIONr_scbond_it2.5833.1963732
X-RAY DIFFRACTIONr_scbond_other2.5813.1943729
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3014.6845525
X-RAY DIFFRACTIONr_long_range_B_refined7.0333.4137702
X-RAY DIFFRACTIONr_long_range_B_other7.02933.4327695
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.222 Å
RfactorNum. reflection% reflection
Rfree0.368 156 -
Rwork0.311 3622 -
obs--96.87 %

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