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- PDB-9j1c: Structure of ConA/NAP-Man -

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Basic information

Entry
Database: PDB / ID: 9j1c
TitleStructure of ConA/NAP-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: 2.43 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/NAP-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)104,29914
Polymers102,4904
Non-polymers1,80910
Water00
1
A: Concanavalin-A
D: Concanavalin-A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,29914
Polymers102,4904
Non-polymers1,80910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area9000 Å2
ΔGint-109 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.379, 61.379, 233.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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-A1EAU / ~{N}2,~{N}6-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]naphthalene-2,6-dicarboxamide


Mass: 714.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H46N2O16 / Feature type: SUBJECT OF INVESTIGATION
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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES monohydrate pH 6.5, 12 % w/v Polyethylene glycol 20,000

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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: 2.43→61.38 Å / Num. obs: 31076 / % possible obs: 96.1 % / Redundancy: 11.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.335 / Rpim(I) all: 0.103 / Rrim(I) all: 0.351 / Χ2: 0.89 / Net I/σ(I): 5.3 / Num. measured all: 352019
Reflection shellResolution: 2.43→2.56 Å / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 3.095 / Num. measured all: 53789 / Num. unique obs: 4725 / CC1/2: 0.447 / Rpim(I) all: 0.967 / Rrim(I) all: 3.245 / Χ2: 0.86 / Net I/σ(I) obs: 1.9

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Processing

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

4p9w


Resolution: 2.43→61.38 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 1581 5.12 %
Rwork0.2113 --
obs0.2149 30904 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→61.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 108 0 7344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097510
X-RAY DIFFRACTIONf_angle_d1.1910240
X-RAY DIFFRACTIONf_dihedral_angle_d16.011064
X-RAY DIFFRACTIONf_chiral_restr0.0641180
X-RAY DIFFRACTIONf_plane_restr0.0081310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.510.3871760.3222738X-RAY DIFFRACTION100
2.51-2.60.39371260.29812787X-RAY DIFFRACTION100
2.6-2.70.31281520.28392794X-RAY DIFFRACTION100
2.7-2.830.38391550.26912764X-RAY DIFFRACTION100
2.83-2.980.35261700.24842758X-RAY DIFFRACTION100
2.98-3.160.31731370.23452787X-RAY DIFFRACTION100
3.16-3.410.32141380.21042822X-RAY DIFFRACTION100
3.41-3.750.24911170.19591981X-RAY DIFFRACTION72
3.75-4.290.22711340.18032346X-RAY DIFFRACTION84
4.29-5.410.22171670.1582756X-RAY DIFFRACTION100
5.41-61.380.22931090.17312790X-RAY DIFFRACTION98

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