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- PDB-8wmk: Structure of ConA/Man2 -

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Basic information

Entry
Database: PDB / ID: 8wmk
TitleStructure of ConA/Man2
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Mannose binding protein / Concanavalin-A
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
ETHANOLAMINE / alpha-D-mannopyranose / : / 4-[3-(4-carboxyphenyl)phenyl]benzoic acid / 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: Rational design of inducing ligands with three-dimensional supramolecular interactions to build protein crystalline frameworks.
Authors: Li, L. / Chen, G.
History
DepositionOct 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 6, 2023Provider: 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)52,23611
Polymers51,2452
Non-polymers9919
Water1,26170
1
A: Concanavalin-A
B: Concanavalin-A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,47122
Polymers102,4904
Non-polymers1,98218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9500 Å2
ΔGint-26 kcal/mol
Surface area34400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.715, 113.841, 83.206
Angle α, β, γ (deg.)90.00, 128.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Author stated: This sequence is a mature form of the provided reference P02866.
Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 77 molecules

#2: Chemical ChemComp-WU0 / 4-[3-(4-carboxyphenyl)phenyl]benzoic acid / [1,1':3',1''-Terphenyl]-4,4''-dicarboxylic acid


Mass: 318.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.28 Å3/Da / Density % sol: 71.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: BL17U1 / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.17→71.83 Å / Num. obs: 45376 / % possible obs: 100 % / Redundancy: 4.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.092 / Rrim(I) all: 0.194 / Χ2: 0.92 / Net I/σ(I): 4.7 / Num. measured all: 196533
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.095 / Num. unique obs: 6599 / CC1/2: 0.496 / Rpim(I) all: 0.595 / Rrim(I) all: 0.251 / Χ2: 0.93 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→71.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.36 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26721 2171 4.9 %RANDOM
Rwork0.22791 ---
obs0.2298 42544 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2---0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.17→71.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 56 73 3747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133758
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173344
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.6535126
X-RAY DIFFRACTIONr_angle_other_deg1.2441.597794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1275472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72623.81168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70215578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2741512
X-RAY DIFFRACTIONr_chiral_restr0.0640.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02764
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_it3.7134.511894
X-RAY DIFFRACTIONr_mcbond_other3.7134.5081893
X-RAY DIFFRACTIONr_mcangle_it6.0526.7572364
X-RAY DIFFRACTIONr_mcangle_other6.0516.7582365
X-RAY DIFFRACTIONr_scbond_it3.6044.731863
X-RAY DIFFRACTIONr_scbond_other3.6054.7281860
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6426.9712761
X-RAY DIFFRACTIONr_long_range_B_refined8.63551.5083887
X-RAY DIFFRACTIONr_long_range_B_other8.63751.5213880
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.173→2.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 159 -
Rwork0.371 3125 -
obs--98 %

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