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- PDB-7elv: Structure of legume lectin domain from Methanocaldococcus jannasc... -

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Basic information

Entry
Database: PDB / ID: 7elv
TitleStructure of legume lectin domain from Methanocaldococcus jannaschii in apo form
Componentslegume lectin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology
Function and homology information


: / Legume lectin beta-barrel domain / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / : / Pectin lyase fold / Pectin lyase fold/virulence factor / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / Uncharacterized protein MJ1396
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSuguna, K. / Khan, F.
Citation
Journal: Proteins / Year: 2023
Title: Crystal structure of an L-type lectin domain from archaea.
Authors: Khan, F. / Kaza, S.
#1: Journal: Glycobiology / Year: 2020
Title: Crystal structures of a beta-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulphide bond-mediated dimeric forms.
Authors: Khan, F. / Kurre, D. / Suguna, K.
History
DepositionApr 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 21, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2958
Polymers22,6621
Non-polymers6347
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-11 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.293, 55.293, 149.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules E

#1: Protein legume lectin


Mass: 22661.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MJ1396
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q58791

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Non-polymers , 5 types, 165 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.4 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 4.6 and 2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→51.86 Å / Num. obs: 38198 / % possible obs: 100 % / Redundancy: 17.1 % / CC1/2: 0.99 / Net I/σ(I): 15.4
Reflection shellResolution: 1.5→1.539 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1837 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BQP

2bqp


Resolution: 1.5→51.86 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.092 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 1934 5.1 %RANDOM
Rwork0.1537 ---
obs0.1548 36174 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.68 Å2 / Biso mean: 17.6 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.5→51.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 38 158 1784
Biso mean--32.85 33.24 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131675
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171462
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.6442295
X-RAY DIFFRACTIONr_angle_other_deg1.5411.5743401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2095210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87725.89778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87615232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.864151
X-RAY DIFFRACTIONr_chiral_restr0.0930.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021898
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02329
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 132 -
Rwork0.221 2620 -
all-2752 -
obs--100 %

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