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Basic information

Entry
Database: PDB / ID: 4oit
TitleStructure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis
ComponentsLysM domain protein
KeywordsSUGAR BINDING PROTEIN / Beta-prism II fold / bacterial lectin / protein-carbohydrate interactions / Beta-Prism II / Carbohydrate binding / Carbohydrate/Sugar
Function / homology
Function and homology information


Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Lysin motif / LysM domain superfamily / LysM domain ...Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Mannose-binding lectin
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPatra, D. / Mishra, P. / Surolia, A. / Vijayan, M.
Citation
Journal: Glycobiology / Year: 2014
Title: Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis.
Authors: Patra, D. / Mishra, P. / Surolia, A. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis
Authors: Patra, D. / Sharma, A. / Chandran, D. / Vijayan, M.
#2: Journal: J.Biosci. / Year: 2007
Title: Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications
Authors: Sharma, A. / Chandran, D. / Singh, D.D. / Vijayan, M.
#3: Journal: Proteins / Year: 2013
Title: Identification of mycobacterial lectins from genomic data
Authors: Abhinav, K.V. / Sharma, A. / Vijayan, M.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: 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
A: LysM domain protein
B: LysM domain protein
C: LysM domain protein
D: LysM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,14915
Polymers50,1674
Non-polymers1,98211
Water2,342130
1
A: LysM domain protein
B: LysM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9857
Polymers25,0842
Non-polymers9015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-22 kcal/mol
Surface area10520 Å2
MethodPISA
2
C: LysM domain protein
D: LysM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1658
Polymers25,0842
Non-polymers1,0816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-24 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 80.080, 56.910
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
LysM domain protein / / Mannose-binding lectin


Mass: 12541.867 Da / Num. of mol.: 4 / Fragment: mannose-binding lectin domain, UNP residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_3662 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QYH7
#2: 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.: 10
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
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2M tri-sodium citrate, 0.1M Na HEPES, 6% glycerol, 30%(w/v) 1,5 diammino pentane dihydrochloride, 60mM mannose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2012 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.24→40 Å / Num. all: 47027 / Num. obs: 19379 / % possible obs: 98.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 6.2
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.38 / Num. unique all: 2766 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native structure

Resolution: 2.24→40 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.882 / SU B: 7.79 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26108 993 5.1 %RANDOM
Rwork0.21999 ---
obs0.22216 18340 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.834 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20.75 Å2
2---1.91 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.24→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 132 130 3450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213376
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.994609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6725.586145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46515504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4061514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022482
X-RAY DIFFRACTIONr_mcbond_it0.3181.52084
X-RAY DIFFRACTIONr_mcangle_it0.5923301
X-RAY DIFFRACTIONr_scbond_it0.78531292
X-RAY DIFFRACTIONr_scangle_it1.3024.51308
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 72 -
Rwork0.257 1297 -
obs-18340 96.61 %

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