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Basic information

Entry
Database: PDB / ID: 4okc
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 Binding
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
Mannose-binding lectin
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: 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


Theoretical massNumber of molelcules
Total (without water)25,0842
Polymers25,0842
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-35 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.960, 42.360, 56.990
Angle α, β, γ (deg.)84.24, 85.91, 84.81
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 12541.867 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2M tri-sodium citrate, 0.1M Na HEPES, 6% glycerol, 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: Jan 10, 2011 / 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: 2.25→40 Å / Num. obs: 9500 / % possible obs: 94.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Num. unique all: 1365 / % possible all: 92.3

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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: 1xd5

1xd5


Resolution: 2.25→35.36 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.171 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26458 659 6.9 %RANDOM
Rwork0.2217 ---
obs0.22475 8839 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0.5 Å2-0.01 Å2
2--0.38 Å22.2 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 0 176 1798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221650
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9532243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24825.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98415272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.981157
X-RAY DIFFRACTIONr_chiral_restr0.1080.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021253
X-RAY DIFFRACTIONr_mcbond_it0.8861.51045
X-RAY DIFFRACTIONr_mcangle_it1.52221662
X-RAY DIFFRACTIONr_scbond_it2.3863605
X-RAY DIFFRACTIONr_scangle_it3.4344.5581
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 45 -
Rwork0.275 631 -
obs-8839 89.06 %

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