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- PDB-7bsn: Mevo lectin complex with 3alpha-mannobiose -

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Basic information

Entry
Database: PDB / ID: 7bsn
TitleMevo lectin complex with 3alpha-mannobiose
Componentslectin
KeywordsSUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure
Function / homology
Function and homology information


Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
3alpha-alpha-mannobiose / alpha-D-mannopyranose / Jacalin-type lectin domain-containing protein
Similarity search - Component
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
A: lectin
B: lectin
C: lectin
D: lectin
E: lectin
F: lectin
G: lectin
H: lectin
I: lectin
J: lectin
K: lectin
L: lectin
M: lectin
N: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,11728
Polymers220,97314
Non-polymers4,14414
Water00
1
A: lectin
B: lectin
C: lectin
D: lectin
E: lectin
F: lectin
G: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,55814
Polymers110,4877
Non-polymers2,0727
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: lectin
I: lectin
J: lectin
K: lectin
L: lectin
M: lectin
N: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,55814
Polymers110,4877
Non-polymers2,0727
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.748, 169.748, 195.738
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
lectin


Mass: 15783.812 Da / Num. of mol.: 14
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 / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
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
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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 296 K / Method: microbatch
Details: 6%(v/v) Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25%(w/v) polyethylene glycol 4000
PH range: 5.8-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.6→97.87 Å / Num. obs: 88208 / % possible obs: 100 % / Redundancy: 24.4 % / CC1/2: 0.74 / Rmerge(I) obs: 0.32 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 24.1 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12714 / CC1/2: 0.775 / % 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: 2.6→85.018 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.22 / Average fsc free: 0.8893 / Average fsc work: 0.9026 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2534 4458 5.06 %
Rwork0.2146 83644 -
all0.217 --
obs-88102 99.976 %
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: 35.117 Å2
Baniso -1Baniso -2Baniso -3
1--2.254 Å2-0 Å2-0 Å2
2---2.254 Å20 Å2
3---4.508 Å2
Refinement stepCycle: LAST / Resolution: 2.6→85.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14641 0 278 0 14919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01315192
X-RAY DIFFRACTIONr_bond_other_d0.0370.01813906
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.66520547
X-RAY DIFFRACTIONr_angle_other_deg2.4521.61332311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.12751940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11224.333607
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.119152484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.611527
X-RAY DIFFRACTIONr_chiral_restr0.0680.22202
X-RAY DIFFRACTIONr_chiral_restr_other0.0190.224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216786
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023019
X-RAY DIFFRACTIONr_nbd_refined0.1740.22101
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.212436
X-RAY DIFFRACTIONr_nbtor_refined0.1650.27170
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.26303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2241
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.222
X-RAY DIFFRACTIONr_nbd_other0.2280.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.27
X-RAY DIFFRACTIONr_mcbond_it3.2043.6847805
X-RAY DIFFRACTIONr_mcbond_other3.2043.6847804
X-RAY DIFFRACTIONr_mcangle_it4.9535.5169730
X-RAY DIFFRACTIONr_mcangle_other4.9545.5179731
X-RAY DIFFRACTIONr_scbond_it3.7444.0477387
X-RAY DIFFRACTIONr_scbond_other3.7444.0477388
X-RAY DIFFRACTIONr_scangle_it5.5855.94310817
X-RAY DIFFRACTIONr_scangle_other5.5845.94310818
X-RAY DIFFRACTIONr_lrange_it7.36242.21615078
X-RAY DIFFRACTIONr_lrange_other7.36342.21515078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.3622840.3166165X-RAY DIFFRACTION100
2.668-2.7410.3333260.3065933X-RAY DIFFRACTION99.984
2.741-2.820.3262860.2755801X-RAY DIFFRACTION99.9836
2.82-2.9070.2763120.2415612X-RAY DIFFRACTION99.9831
2.907-3.0020.3022680.2285490X-RAY DIFFRACTION100
3.002-3.1070.2692540.2155304X-RAY DIFFRACTION100
3.107-3.2250.2712770.2115100X-RAY DIFFRACTION99.9814
3.225-3.3560.2542770.2094911X-RAY DIFFRACTION99.9615
3.356-3.5050.2362550.2064723X-RAY DIFFRACTION99.9799
3.505-3.6760.262420.2244520X-RAY DIFFRACTION100
3.676-3.8750.2422620.2094305X-RAY DIFFRACTION99.9781
3.875-4.110.2422450.2024055X-RAY DIFFRACTION99.9767
4.11-4.3930.2151880.1773885X-RAY DIFFRACTION99.9509
4.393-4.7450.1982170.1573573X-RAY DIFFRACTION99.9736
4.745-5.1970.1941870.1613316X-RAY DIFFRACTION100
5.197-5.8090.2361710.1953015X-RAY DIFFRACTION100
5.809-6.7050.2561310.2222707X-RAY DIFFRACTION99.9648
6.705-8.2070.2571180.2222321X-RAY DIFFRACTION99.8772
8.207-11.5830.2311020.2251816X-RAY DIFFRACTION99.8958
11.583-13.50.473560.3361092X-RAY DIFFRACTION99.8261

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