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- PDB-7bt8: Mevo lectin complex with mannotriose -

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Basic information

Entry
Database: PDB / ID: 7bt8
TitleMevo lectin complex with mannotriose
Componentslectin
KeywordsSUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure
Function / homologyJacalin-like lectin domain superfamily / Jacalin-type lectin domain-containing protein
Function and homology information
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2016/005205 India
CitationJournal: Glycobiology / Year: 2021
Title: Structural and related studies on Mevo lectin from Methanococcus voltae A3: the first thorough characterization of an archeal lectin and its interactions.
Authors: Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M.
History
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,90721
Polymers106,4717
Non-polymers2,43614
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.770, 157.220, 163.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.36 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 6
Details: 6%(v/v) Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25%(w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→54.39 Å / Num. obs: 39930 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.85 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5790 / CC1/2: 0.68 / % possible all: 100

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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: 2.7→54.39 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.557 / ESU R Free: 0.286
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2336 2027 5.086 %
Rwork0.2099 --
all0.211 --
obs-39930 99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.967 Å2
Baniso -1Baniso -2Baniso -3
1-3.156 Å20 Å20 Å2
2---0.532 Å20 Å2
3----2.624 Å2
Refinement stepCycle: LAST / Resolution: 2.7→54.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7220 0 162 61 7443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137505
X-RAY DIFFRACTIONr_bond_other_d0.0370.0186867
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.65910131
X-RAY DIFFRACTIONr_angle_other_deg2.4271.60615947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4375956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26424.482299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.628151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9431512
X-RAY DIFFRACTIONr_chiral_restr0.0640.21073
X-RAY DIFFRACTIONr_chiral_restr_other0.0130.29
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028276
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021484
X-RAY DIFFRACTIONr_nbd_refined0.1780.21017
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.26273
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23537
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2185
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1190.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2980.29
X-RAY DIFFRACTIONr_nbd_other0.2710.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.26
X-RAY DIFFRACTIONr_mcbond_it3.4253.9993854
X-RAY DIFFRACTIONr_mcbond_other3.4263.9983853
X-RAY DIFFRACTIONr_mcangle_it5.3515.9874800
X-RAY DIFFRACTIONr_mcangle_other5.3515.9874801
X-RAY DIFFRACTIONr_scbond_it3.9234.3713651
X-RAY DIFFRACTIONr_scbond_other3.9224.3713652
X-RAY DIFFRACTIONr_scangle_it5.8826.3995331
X-RAY DIFFRACTIONr_scangle_other5.8826.45332
X-RAY DIFFRACTIONr_lrange_it9.13177.12430010
X-RAY DIFFRACTIONr_lrange_other9.13177.12430004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3781210.3242827X-RAY DIFFRACTION100
2.77-2.8460.3411450.3132695X-RAY DIFFRACTION99.8594
2.846-2.9280.2721610.2832642X-RAY DIFFRACTION99.8931
2.928-3.0190.3021420.2592541X-RAY DIFFRACTION99.7769
3.019-3.1170.2761700.2562457X-RAY DIFFRACTION99.5453
3.117-3.2270.2561290.2352386X-RAY DIFFRACTION100
3.227-3.3480.2241300.2172329X-RAY DIFFRACTION99.2733
3.348-3.4850.2311210.2082267X-RAY DIFFRACTION99.005
3.485-3.640.2571010.2242144X-RAY DIFFRACTION99.911
3.64-3.8170.214880.22058X-RAY DIFFRACTION98.7121
3.817-4.0240.2321190.21958X-RAY DIFFRACTION98.3894
4.024-4.2670.184880.1721861X-RAY DIFFRACTION98.7836
4.267-4.5610.159810.1491734X-RAY DIFFRACTION98.5342
4.561-4.9260.153700.1431656X-RAY DIFFRACTION97.9569
4.926-5.3950.187830.1611477X-RAY DIFFRACTION97.561
5.395-6.0310.193630.1851370X-RAY DIFFRACTION97.0867
6.031-6.960.232650.1961186X-RAY DIFFRACTION95.0608
6.96-8.5160.211670.2997X-RAY DIFFRACTION95.7696
8.516-12.010.219500.207800X-RAY DIFFRACTION94.1307
12.01-13.50.397330.3445X-RAY DIFFRACTION88.0295

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