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- PDB-8i7q: Cobalt and Calcium coordinated Concanavalin A at pH 7.4 from Cana... -

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Basic information

Entry
Database: PDB / ID: 8i7q
TitleCobalt and Calcium coordinated Concanavalin A at pH 7.4 from Canavalia ensiformis
ComponentsConcanavalin A
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology:
Function and homology information
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsHwang, Y. / Jeong, J.H. / Lee, S.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015M3D3A1A01064876 Korea, Republic Of
Ministry of Education (MoE, Korea)2017R1A6A1A03015876 Korea, Republic Of
CitationJournal: Dalton Trans / Year: 2024
Title: Selective interactions of Co 2+ -Ca 2+ -concanavalin A with high mannose N -glycans.
Authors: Hwang, Y. / Jeong, J.H. / Lee, D.H. / Lee, S.J.
History
DepositionFeb 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6913
Polymers25,5921
Non-polymers992
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.820, 86.050, 88.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Concanavalin A


Mass: 25592.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.01 M cobalt(II) chloride hexahydrate, 0.1 M MES monohydrate pH 6.5, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 2, 2022 / Details: In-vacuum Undulator
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→27.93 Å / Num. obs: 5904 / % possible obs: 99.9 % / Redundancy: 2 % / Rrim(I) all: 0.0702 / Net I/σ(I): 8.2
Reflection shellResolution: 2.83→2.93 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 588 / Rrim(I) all: 0.413

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→27.93 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2971 585 9.94 %RANDOM
Rwork0.2577 ---
obs0.2616 5883 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.83→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 2 19 1828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041851
X-RAY DIFFRACTIONf_angle_d0.8112524
X-RAY DIFFRACTIONf_dihedral_angle_d13.165250
X-RAY DIFFRACTIONf_chiral_restr0.051290
X-RAY DIFFRACTIONf_plane_restr0.005326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-3.110.40761440.37181304X-RAY DIFFRACTION99
3.11-3.560.34571380.28981297X-RAY DIFFRACTION100
3.57-4.490.28311490.24561314X-RAY DIFFRACTION100
4.49-27.930.25931540.22311383X-RAY DIFFRACTION100

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