[English] 日本語
Yorodumi
- PDB-7mga: Concanavalin A bound to a DNA glycoconjugate, Man-AAATTT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mga
TitleConcanavalin A bound to a DNA glycoconjugate, Man-AAATTT
Components
  • Concanavalin-A
  • DNA (5'-D(P*AP*AP*AP*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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,01012
Polymers54,8594
Non-polymers1,1518
Water5,188288
1
A: Concanavalin-A
B: Concanavalin-A
C: DNA (5'-D(P*AP*AP*AP*TP*TP*T)-3')
D: DNA (5'-D(P*AP*AP*AP*TP*TP*T)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)112,02124
Polymers109,7198
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)65.090, 77.780, 126.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
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

-
Components

-
Protein / DNA chain / Sugars , 3 types, 6 molecules ABCD

#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
#2: DNA chain DNA (5'-D(P*AP*AP*AP*TP*TP*T)-3')


Mass: 1807.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: 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

-
Non-polymers , 4 types, 294 molecules

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


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and Man-AAATTT (64 uM) + 1 uL crystallization condition (Helix screen, condition A3: 0.1 M sodium chloride, 0.05 M lithium chloride, 0. ...Details: Sitting drop comprising 1 uL of Concanavalin A (32 uM) and Man-AAATTT (64 uM) + 1 uL crystallization condition (Helix screen, condition A3: 0.1 M sodium chloride, 0.05 M lithium chloride, 0.01 M magnesium chloride hexahydrate, 0.05 M MES (pH 6.5), 25% v/v PEG 400). Reservoir contained 70 uL of crystallization condition

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2→57.9 Å / Num. obs: 37677 / % possible obs: 90.1 % / Redundancy: 3.16 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 4.6593
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.7 / Num. unique obs: 5282 / % possible all: 83.4

-
Processing

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

1jbc


Resolution: 2→57.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.044 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2002 5 %RANDOM
Rwork0.196 ---
obs0.198 37677 90.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--1.32 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2→57.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 246 68 288 4067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133905
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173336
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.5995348
X-RAY DIFFRACTIONr_angle_other_deg1.3951.6317754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1245459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46323.503157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47515511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8371510
X-RAY DIFFRACTIONr_chiral_restr0.1760.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
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_it2.4392.5941850
X-RAY DIFFRACTIONr_mcbond_other2.4362.5921849
X-RAY DIFFRACTIONr_mcangle_it3.6263.872303
X-RAY DIFFRACTIONr_mcangle_other3.6273.8712304
X-RAY DIFFRACTIONr_scbond_it3.7373.4032055
X-RAY DIFFRACTIONr_scbond_other3.7363.4032056
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5445.0053042
X-RAY DIFFRACTIONr_long_range_B_refined7.52554.49216208
X-RAY DIFFRACTIONr_long_range_B_other7.47254.34116026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7005 / 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→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 174 -
Rwork0.274 2970 -
obs--97.97 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more