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- PDB-7ded: Mevo lectin complex with mannoheptose (Man7) -

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Basic information

Entry
Database: PDB / ID: 7ded
TitleMevo lectin complex with mannoheptose (Man7)
Componentslectin
KeywordsSUGAR BINDING PROTEIN / beta-prism I fold / Mevo lectin / heptamer / ring shape structure
Function / homologyJacalin-like lectin domain superfamily / alpha-D-mannopyranose / Jacalin-type lectin domain-containing protein
Function and homology information
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.228 Å
AuthorsSivaji, N. / Surolia, A. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2016/005205 India
Citation
Journal: Glycobiology / Year: 2021
Title: Mevo lectin specificity toward high-mannose structures with terminal alpha Man(1,2) alpha Man residues and its implication to inhibition of the entry of Mycobacterium tuberculosis into macrophages.
Authors: Sivaji, N. / Harish, N. / Singh, S. / Singh, A. / Vijayan, M. / Surolia, A.
#1: Journal: Glycobiology / Year: 2020
Title: Structural and related studies on Mevo lectin from Methanococcus voltae A3. The first thorough characterisation of an archeal lectin and its interactions.
Authors: Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M.
#2: Journal: Proteins / Year: 2016
Title: Archeal lectins: An identification through a genomic search.
Authors: Abhinav, K.V. / Samuel, E. / Vijayan, M.
History
DepositionNov 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: lectin
E: lectin
A: lectin
B: lectin
C: lectin
G: lectin
F: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,55526
Polymers106,4717
Non-polymers4,08419
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint108 kcal/mol
Surface area39120 Å2
Unit cell
Length a, b, c (Å)168.350, 168.350, 104.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
lectin /


Mass: 15210.124 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus voltae (strain ATCC BAA-1334 / A3) (archaea)
Strain: ATCC BAA-1334 / A3 / Gene: Mvol_0737 / Production host: Escherichia coli (E. coli) / References: UniProt: D7DTD6
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a1122h-1a_1-5]/1-1-1-1-1-1/a3-b1_a6-e1_b2-c1_c2-d1_e3-f1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / 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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.49 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6
Details: Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 14, 2020
RadiationMonochromator: Cu K / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→61.18 Å / Num. obs: 73523 / % possible obs: 99.7 % / Redundancy: 19.2 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.39 / Rpim(I) all: 0.091 / Net I/σ(I): 7.8
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10366 / CC1/2: 0.524 / Rpim(I) all: 0.196 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BSB

7bsb


Resolution: 2.228→59.592 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.885 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.217 / Average fsc free: 0.8348 / Average fsc work: 0.841 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2667 3622 4.929 %
Rwork0.2465 69860 -
all0.248 --
obs-73482 99.383 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.494 Å2-0 Å20 Å2
2---1.494 Å20 Å2
3---2.988 Å2
Refinement stepCycle: LAST / Resolution: 2.228→59.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7427 0 273 127 7827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137831
X-RAY DIFFRACTIONr_bond_other_d0.0360.0187224
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.68510558
X-RAY DIFFRACTIONr_angle_other_deg2.4051.62816854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5975972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08224.606317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4071513
X-RAY DIFFRACTIONr_chiral_restr0.0660.21136
X-RAY DIFFRACTIONr_chiral_restr_other0.0020.218
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028471
X-RAY DIFFRACTIONr_gen_planes_other0.020.021514
X-RAY DIFFRACTIONr_nbd_refined0.1750.21043
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.26387
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23776
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2178
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0940.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.214
X-RAY DIFFRACTIONr_nbd_other0.2220.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.211
X-RAY DIFFRACTIONr_mcbond_it2.3552.0183909
X-RAY DIFFRACTIONr_mcbond_other2.3552.0173908
X-RAY DIFFRACTIONr_mcangle_it3.8373.0164874
X-RAY DIFFRACTIONr_mcangle_other3.8373.0174875
X-RAY DIFFRACTIONr_scbond_it2.5422.2843922
X-RAY DIFFRACTIONr_scbond_other2.5422.2843923
X-RAY DIFFRACTIONr_scangle_it3.9723.3315684
X-RAY DIFFRACTIONr_scangle_other3.9723.3315685
X-RAY DIFFRACTIONr_lrange_it5.58823.2797825
X-RAY DIFFRACTIONr_lrange_other5.58823.2847822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.228-2.2860.3962200.3834746X-RAY DIFFRACTION91.8439
2.286-2.3480.3752570.3474968X-RAY DIFFRACTION100
2.348-2.4160.3482430.3374873X-RAY DIFFRACTION100
2.416-2.4910.3782390.3394735X-RAY DIFFRACTION100
2.491-2.5720.3152420.3194590X-RAY DIFFRACTION100
2.572-2.6620.3242150.3164447X-RAY DIFFRACTION100
2.662-2.7630.3442110.34328X-RAY DIFFRACTION100
2.763-2.8760.2932260.2764112X-RAY DIFFRACTION100
2.876-3.0030.2851880.253998X-RAY DIFFRACTION99.9284
3.003-3.150.2562220.2433770X-RAY DIFFRACTION99.9499
3.15-3.320.2351910.2143613X-RAY DIFFRACTION99.9474
3.32-3.5210.2181920.1913430X-RAY DIFFRACTION100
3.521-3.7640.2211610.1963250X-RAY DIFFRACTION100
3.764-4.0660.231320.1753056X-RAY DIFFRACTION100
4.066-4.4530.191510.1642780X-RAY DIFFRACTION100
4.453-4.9780.1631530.1412549X-RAY DIFFRACTION100
4.978-5.7460.1671180.162257X-RAY DIFFRACTION100
5.746-7.0340.2331100.1941936X-RAY DIFFRACTION100
7.034-9.930.213980.2131519X-RAY DIFFRACTION100
9.93-11.90410.342530.333903X-RAY DIFFRACTION99.2731

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