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- PDB-7mgc: Concanavalin A bound to a DNA glycoconjugate, G(Man-T)AC -

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Basic information

Entry
Database: PDB / ID: 7mgc
TitleConcanavalin A bound to a DNA glycoconjugate, G(Man-T)AC
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN/DNA / Lectin / DNA complex / SUGAR BINDING PROTEIN / 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
methyl alpha-D-mannopyranoside / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)103,64616
Polymers102,4904
Non-polymers1,15712
Water70339
1
A: Concanavalin-A
C: Concanavalin-A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)103,64616
Polymers102,4904
Non-polymers1,15712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area8870 Å2
ΔGint-107 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.330, 117.340, 122.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASPAA1 - 2351 - 235
21ALAALAASPASPBB1 - 2351 - 235
12ALAALAASNASNAA1 - 2371 - 237
22ALAALAASNASNCC1 - 2371 - 237
13ASPASPASNASNAA2 - 2372 - 237
23ASPASPASNASNDD2 - 2372 - 237
14ALAALAASPASPBB1 - 2351 - 235
24ALAALAASPASPCC1 - 2351 - 235
15ASPASPALAALABB2 - 2362 - 236
25ASPASPALAALADD2 - 2362 - 236
16ASPASPASNASNCC2 - 2372 - 237
26ASPASPASNASNDD2 - 2372 - 237

NCS ensembles :
ID
1
2
3
4
5
6

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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: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop comprising 1 uL of Concanavalin A (40 uM) and G(Man-T)AC (160 uM) + 1 uL crystallization condition (Helix screen, condition H6: 0.1 M potassium chloride, 0.002 M spermine ...Details: Sitting drop comprising 1 uL of Concanavalin A (40 uM) and G(Man-T)AC (160 uM) + 1 uL crystallization condition (Helix screen, condition H6: 0.1 M potassium chloride, 0.002 M spermine tetrahydrochloride, 0.05 M bis-Tris (pH 7), 15% w/v PEG 2000 MME). 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-D / Wavelength: 1.0782 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.92→84.7 Å / Num. obs: 19900 / % possible obs: 94.25 % / Redundancy: 7.39 % / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.16 / Net I/σ(I): 4.1051
Reflection shellResolution: 2.92→3.08 Å / Redundancy: 7.95 % / Rmerge(I) obs: 0.56 / Num. unique obs: 3178 / Rrim(I) all: 0.599 / % possible all: 99.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNA

5cna


Resolution: 2.92→84.7 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 26.133 / SU ML: 0.456 / Cross valid method: THROUGHOUT / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE AUTHORS STATE THAT THE COORDINATES OF THE DNA COULD NOT BE RESOLVED IN THE ELECTRON DENSITY, PUTATIVELY DUE TO DISORDER, BUT ITS BINDING IS CONFIRMED BY THE OBSERVATION OF THE ...Details: THE AUTHORS STATE THAT THE COORDINATES OF THE DNA COULD NOT BE RESOLVED IN THE ELECTRON DENSITY, PUTATIVELY DUE TO DISORDER, BUT ITS BINDING IS CONFIRMED BY THE OBSERVATION OF THE METHYLMANNOSE (THIS IS ACTUALLY PART OF A MANNOSE-SQUARAMIDE LINKER COVALENTLY BOUND TO THE DNA). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27679 1072 5.1 %RANDOM
Rwork0.22927 ---
obs0.23168 19900 94.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.932 Å2
Baniso -1Baniso -2Baniso -3
1-6.25 Å20 Å2-0 Å2
2---7.81 Å20 Å2
3---1.56 Å2
Refinement stepCycle: 1 / Resolution: 2.92→84.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6859 0 60 39 6958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176089
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6389650
X-RAY DIFFRACTIONr_angle_other_deg1.2461.57814125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5965929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41523.833300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68915974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2161520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021442
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_it4.1035.3833731
X-RAY DIFFRACTIONr_mcbond_other4.1025.3823730
X-RAY DIFFRACTIONr_mcangle_it6.5438.0674652
X-RAY DIFFRACTIONr_mcangle_other6.5438.0674653
X-RAY DIFFRACTIONr_scbond_it3.775.4773330
X-RAY DIFFRACTIONr_scbond_other3.7695.4773330
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1218.144998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A67830.08
12B67830.08
21A66630.07
22C66630.07
31A66660.07
32D66660.07
41B66620.07
42C66620.07
51B67310.07
52D67310.07
61C68380.05
62D68380.05
LS refinement shellResolution: 2.924→3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 91 -
Rwork0.333 1507 -
obs--99.69 %

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