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- PDB-7mg4: Concanavalin A crystallized in the presence of Gal-ATAT -

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Basic information

Entry
Database: PDB / ID: 7mg4
TitleConcanavalin A crystallized in the presence of Gal-ATAT
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN/DNA / Lectin / SUGAR BINDING PROTEIN-DNA complex
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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPartridge, B.E. / Winegar, P.H. / Mirkin, C.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N00014-15-1-0043 United States
Department of Defense (DOD, United States)FA9550-16-1-0150 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Redefining Protein Interfaces within Protein Single Crystals with DNA.
Authors: Partridge, B.E. / Winegar, P.H. / Han, Z. / Mirkin, C.A.
History
DepositionApr 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,7173
Polymers25,6221
Non-polymers952
Water3,783210
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)102,87012
Polymers102,4904
Non-polymers3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area9040 Å2
ΔGint-128 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.630, 86.030, 89.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21A-560-

HOH

31A-566-

HOH

41A-605-

HOH

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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-MN / MANGANESE (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and Gal-ATAT (128 uM) + 1 uL crystallization condition (Helix screen, condition H9: 0.1 M potassium chloride, 0.002 M spermine ...Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and Gal-ATAT (128 uM) + 1 uL crystallization condition (Helix screen, condition H9: 0.1 M potassium chloride, 0.002 M spermine tetrahydrochloride, 0.05 M bis-Tris (pH 7.5), 7% w/v PEG 8000). Reservoir contained 70 uL of crystallization condition.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→61.93 Å / Num. obs: 14558 / % possible obs: 93.4 % / Redundancy: 7.66 % / Rmerge(I) obs: 0.114 / Rsym value: 0.123 / Net I/σ(I): 3.0684
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.05 % / Rmerge(I) obs: 0.45 / Num. unique obs: 1983 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBC

1jbc


Resolution: 2→61.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.511 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The authors state that the electron density was not observed for the molecule Gal-ATAT, though it was present in the crystallization solution from which this crystal of ConA was obtained. ...Details: The authors state that the electron density was not observed for the molecule Gal-ATAT, though it was present in the crystallization solution from which this crystal of ConA was obtained. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 749 4.9 %RANDOM
Rwork0.179 ---
obs0.182 14558 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---0.34 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2→61.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 2 210 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131811
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171596
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6312476
X-RAY DIFFRACTIONr_angle_other_deg1.3351.573706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7035236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72723.89677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84815263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.918155
X-RAY DIFFRACTIONr_chiral_restr0.0660.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
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_it1.6181.984947
X-RAY DIFFRACTIONr_mcbond_other1.6141.983946
X-RAY DIFFRACTIONr_mcangle_it2.4232.9641182
X-RAY DIFFRACTIONr_mcangle_other2.4222.9661183
X-RAY DIFFRACTIONr_scbond_it1.9382.124863
X-RAY DIFFRACTIONr_scbond_other1.9342.118860
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9673.1161293
X-RAY DIFFRACTIONr_long_range_B_refined5.52124.3011951
X-RAY DIFFRACTIONr_long_range_B_other5.25123.9471919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 57 -
Rwork0.223 1126 -
obs--99.92 %

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