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- PDB-7mg2: Concanavalin A crystallized in the presence of Man-8 -

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Basic information

Entry
Database: PDB / ID: 7mg2
TitleConcanavalin A crystallized in the presence of Man-8
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: 1.8 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
Water4,666259
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 area8410 Å2
ΔGint-127 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.420, 86.130, 89.500
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-429-

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.: 259 / 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: 46.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and mannose-squaramide (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium ...Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and mannose-squaramide (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium chloride hexahydrate, 0.05 M MES (pH 6.5), 17% w/v PEG 4000). 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: 1.8→62.06 Å / Num. obs: 21234 / % possible obs: 99.8 % / Redundancy: 9.11 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 2.5465
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.95 % / Rmerge(I) obs: 0.63 / Num. unique obs: 3218 / % possible all: 100

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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: 1.8→62.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.304 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The authors state that the electron density was not observed for the molecule Man-8, 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 Man-8, 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
Rfree0.23 1114 5 %RANDOM
Rwork0.184 ---
obs0.186 21234 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: 17.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---0.34 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→62.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 2 259 2022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131813
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171618
X-RAY DIFFRACTIONr_angle_refined_deg1.561.632475
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5723765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3595233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3723.97478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85215273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.881155
X-RAY DIFFRACTIONr_chiral_restr0.0660.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
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_it1.4631.693938
X-RAY DIFFRACTIONr_mcbond_other1.4581.691937
X-RAY DIFFRACTIONr_mcangle_it2.2612.5271169
X-RAY DIFFRACTIONr_mcangle_other2.262.5291170
X-RAY DIFFRACTIONr_scbond_it1.9711.885874
X-RAY DIFFRACTIONr_scbond_other1.9651.879871
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.022.7391305
X-RAY DIFFRACTIONr_long_range_B_refined5.94321.6661977
X-RAY DIFFRACTIONr_long_range_B_other5.57720.9331924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 70 -
Rwork0.225 1553 -
obs--100 %

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