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- PDB-7mg9: Concanavalin A bound to DNA glycoconjugates, Man-TTTT and Man-AAAA -

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Basic information

Entry
Database: PDB / ID: 7mg9
TitleConcanavalin A bound to DNA glycoconjugates, Man-TTTT and Man-AAAA
Components
  • Concanavalin-A
  • DNA (5'-D(P*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*T)-3')
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, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / : / Chem-SQ0 / DNA / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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: 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 / 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: DNA (5'-D(P*AP*AP*AP*A)-3')
D: DNA (5'-D(P*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,77612
Polymers53,6244
Non-polymers1,1518
Water2,702150
1
A: Concanavalin-A
B: Concanavalin-A
C: DNA (5'-D(P*AP*AP*AP*A)-3')
D: DNA (5'-D(P*TP*TP*TP*T)-3')
hetero molecules

A: Concanavalin-A
B: Concanavalin-A
C: DNA (5'-D(P*AP*AP*AP*A)-3')
D: DNA (5'-D(P*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,55124
Polymers107,2498
Non-polymers2,30216
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)65.979, 70.180, 124.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-405-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 237 / Label seq-ID: 1 - 237

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*AP*AP*AP*A)-3')


Mass: 1207.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*T)-3')


Mass: 1171.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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 / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#6: 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 , 4 types, 156 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-SQ0 / 3-{[2-(2-hydroxyethoxy)ethyl]amino}-4-[(6-hydroxyhexyl)amino]cyclobut-3-ene-1,2-dione


Mass: 300.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM), Man-TTTT (64 uM), and Man-AAAA (64 uM) + 1 uL crystallization condition (Helix screen, condition B5: 0.1 M lithium chloride, 0.01 M ...Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM), Man-TTTT (64 uM), and Man-AAAA (64 uM) + 1 uL crystallization condition (Helix screen, condition B5: 0.1 M lithium chloride, 0.01 M manganese(II) chloride tetrahydrate, 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-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→70.18 Å / Num. obs: 17243 / % possible obs: 93.1 % / Redundancy: 3.25 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.9147
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Num. unique obs: 2376 / % possible all: 86

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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: 2.55→70.18 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.794 / SU B: 18.314 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 0.892 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.314 899 5 %RANDOM
Rwork0.25 ---
obs0.253 17243 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--1.28 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.55→70.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 164 68 150 3778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133752
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173153
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6085126
X-RAY DIFFRACTIONr_angle_other_deg1.2631.6117316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0975461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00923.205156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94715477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4451511
X-RAY DIFFRACTIONr_chiral_restr0.1530.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
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_it2.333.3071852
X-RAY DIFFRACTIONr_mcbond_other2.3233.3051851
X-RAY DIFFRACTIONr_mcangle_it3.8264.9552306
X-RAY DIFFRACTIONr_mcangle_other3.8284.9572307
X-RAY DIFFRACTIONr_scbond_it2.8333.971900
X-RAY DIFFRACTIONr_scbond_other2.8333.9691901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4895.8842816
X-RAY DIFFRACTIONr_long_range_B_refined7.57966.7415226
X-RAY DIFFRACTIONr_long_range_B_other7.55966.72815184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6771 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 69 -
Rwork0.361 1291 -
obs--96.87 %

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