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- PDB-9j1a: Structure of ConA without ligand -

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Basic information

Entry
Database: PDB / ID: 9j1a
TitleStructure of ConA without ligand
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Mannose / 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 / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 without ligand
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

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Assembly

Deposited unit
A: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8094
Polymers25,6221
Non-polymers1873
Water2,198122
1
A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,23816
Polymers102,4904
Non-polymers74812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11490 Å2
ΔGint-109 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.239, 87.413, 88.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.8M Ammonium Sulfate, 0.1M MES pH 6.5, 0.01M Cobalt Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.48→31.19 Å / Num. obs: 40754 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.033 / Rrim(I) all: 0.113 / Χ2: 0.76 / Net I/σ(I): 10.2
Reflection shellResolution: 1.48→1.52 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.434 / Num. measured all: 21079 / Num. unique obs: 2977 / CC1/2: 0.741 / Rpim(I) all: 0.575 / Rrim(I) all: 1.548 / Χ2: 0.69 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→31.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.685 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21318 2010 4.9 %RANDOM
Rwork0.18386 ---
obs0.18537 38671 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.931 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.48→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 8 122 1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131856
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171660
X-RAY DIFFRACTIONr_angle_refined_deg1.731.6322529
X-RAY DIFFRACTIONr_angle_other_deg1.5141.5743867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6635236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38723.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90915289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.741156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
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_it1.7951.608947
X-RAY DIFFRACTIONr_mcbond_other1.7841.606946
X-RAY DIFFRACTIONr_mcangle_it2.8572.4071182
X-RAY DIFFRACTIONr_mcangle_other2.8582.4091183
X-RAY DIFFRACTIONr_scbond_it3.0261.947908
X-RAY DIFFRACTIONr_scbond_other3.0241.948909
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5262.7751348
X-RAY DIFFRACTIONr_long_range_B_refined5.86519.8871941
X-RAY DIFFRACTIONr_long_range_B_other5.85119.7491926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 133 -
Rwork0.333 2831 -
obs--99.63 %

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