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- PDB-7bt9: Mevo lectin complex with alpha-mannose -

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Basic information

Entry
Database: PDB / ID: 7bt9
TitleMevo lectin complex with alpha-mannose
Componentslectin
KeywordsSUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure
Function / homologyJacalin-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 / alpha-D-mannopyranose / Jacalin-type lectin domain-containing protein
Function and homology information
Biological speciesMethanococcus voltae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
H: lectin
I: lectin
J: lectin
K: lectin
L: lectin
M: lectin
N: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,49628
Polymers220,97314
Non-polymers2,52214
Water00
1
B: lectin
G: lectin
A: lectin
D: lectin
E: lectin
F: lectin
C: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,74814
Polymers110,4877
Non-polymers1,2617
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)111,74814
Polymers110,4877
Non-polymers1,2617
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.849, 168.849, 193.639
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: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
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
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: 2.82 Å3/Da / Density % sol: 56.36 %
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: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→96.82 Å / Num. obs: 101188 / % possible obs: 98.4 % / Redundancy: 10.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.22 / Net I/σ(I): 6.1
Reflection shellResolution: 2.45→2.58 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13609 / CC1/2: 0.75

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Processing

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

7bsm


Resolution: 2.45→84.567 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.285 / WRfactor Rwork: 0.245 / Average fsc free: 0.7787 / Average fsc work: 0.797 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.279
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2837 5072 5.028 %
Rwork0.2423 95803 -
all0.244 --
obs-100875 98.115 %
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: 36.231 Å2
Baniso -1Baniso -2Baniso -3
1--4.301 Å20 Å20 Å2
2---4.301 Å20 Å2
3---8.602 Å2
Refinement stepCycle: LAST / Resolution: 2.45→84.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14576 0 168 0 14744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01315004
X-RAY DIFFRACTIONr_bond_other_d0.0370.01713803
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.65320272
X-RAY DIFFRACTIONr_angle_other_deg2.4771.59532020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.46751932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08124.243601
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34152475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9231528
X-RAY DIFFRACTIONr_chiral_restr0.0730.22146
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216695
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023008
X-RAY DIFFRACTIONr_nbd_refined0.1830.22371
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.212865
X-RAY DIFFRACTIONr_nbtor_refined0.1790.27073
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.26438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2300
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.218
X-RAY DIFFRACTIONr_nbd_other0.2790.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.25
X-RAY DIFFRACTIONr_mcbond_it3.4133.8027776
X-RAY DIFFRACTIONr_mcbond_other3.4133.8027775
X-RAY DIFFRACTIONr_mcangle_it5.2865.6979692
X-RAY DIFFRACTIONr_mcangle_other5.2865.6979693
X-RAY DIFFRACTIONr_scbond_it3.7024.1287228
X-RAY DIFFRACTIONr_scbond_other3.7024.1287228
X-RAY DIFFRACTIONr_scangle_it5.6916.05710580
X-RAY DIFFRACTIONr_scangle_other5.6916.05710581
X-RAY DIFFRACTIONr_lrange_it8.95672.93860157
X-RAY DIFFRACTIONr_lrange_other8.95772.93660153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5140.4043460.3866416X-RAY DIFFRACTION90.0999
2.514-2.5820.3933480.3796485X-RAY DIFFRACTION93.8599
2.582-2.6570.4113720.366433X-RAY DIFFRACTION95.3482
2.657-2.7390.3883050.3376436X-RAY DIFFRACTION97.3711
2.739-2.8290.3153330.2856322X-RAY DIFFRACTION99.136
2.829-2.9280.3143160.2566168X-RAY DIFFRACTION99.6618
2.928-3.0390.2883050.2415969X-RAY DIFFRACTION99.8727
3.039-3.1630.2773100.2215723X-RAY DIFFRACTION99.9337
3.163-3.3030.2942800.2345536X-RAY DIFFRACTION99.8798
3.303-3.4640.2612930.225281X-RAY DIFFRACTION99.7495
3.464-3.6510.2732700.2345000X-RAY DIFFRACTION99.6973
3.651-3.8730.2882340.2284787X-RAY DIFFRACTION99.7219
3.873-4.140.2722560.2194469X-RAY DIFFRACTION99.4946
4.14-4.4710.2052180.1844182X-RAY DIFFRACTION99.525
4.471-4.8970.2341990.1733862X-RAY DIFFRACTION99.4855
4.897-5.4740.2552010.1983528X-RAY DIFFRACTION99.7059
5.474-6.3190.2791540.2423145X-RAY DIFFRACTION99.8185
6.319-7.7350.251460.2312683X-RAY DIFFRACTION99.8941
7.735-10.9180.2441060.2392128X-RAY DIFFRACTION99.9106
10.918-12.70.278800.3261250X-RAY DIFFRACTION99.8499

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