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- PDB-9c4i: Centrolobium microchaete seed lectin (CML) complexed with Man1-3M... -

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Basic information

Entry
Database: PDB / ID: 9c4i
TitleCentrolobium microchaete seed lectin (CML) complexed with Man1-3Man-OMe
ComponentsMannose-specific lectin CML-1
KeywordsSUGAR BINDING PROTEIN / lectin / Dalbergieae tribe
Function / homology
Function and homology information


D-mannose binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / Mannose-specific lectin CML-2
Similarity search - Component
Biological speciesCentrolobium microchaete (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsNascimento, K.S. / Pinto-Junior, V.R. / Lima, F.E.O. / Osterne, V.J.S. / Oliveira, M.V. / Ferreira, V.M.S. / Cavada, B.S.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Coordination for the Improvement of Higher Education Personnel Brazil
CitationJournal: To Be Published
Title: Centrolobium microchaete seed lectin (CML) complexed with Man1-3Man-OMe
Authors: Nascimento, K.S. / Pinto-Junior, V.R. / Lima, F.E.O. / Osterne, V.J.S. / Oliveira, M.V. / Ferreira, V.M.S. / Cavada, B.S.
History
DepositionJun 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose-specific lectin CML-1
B: Mannose-specific lectin CML-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,29822
Polymers53,2432
Non-polymers2,05520
Water13,655758
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-130 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.623, 41.981, 94.760
Angle α, β, γ (deg.)90.00, 102.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mannose-specific lectin CML-1


Mass: 26621.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Centrolobium microchaete (plant) / References: UniProt: C0HK20

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-3DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 774 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM ammonium sulfate, 100 mM HEPES pH 7.5, 25% PEG 3350
PH range: 7.2-7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.3→46.22 Å / Num. obs: 138969 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Net I/σ(I): 17.3
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 19912 / CC1/2: 0.949 / Rpim(I) all: 0.228 / Rrim(I) all: 0.581 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→43.42 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 6934 4.99 %
Rwork0.1723 --
obs0.1733 138823 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.37 Å2
Refinement stepCycle: LAST / Resolution: 1.3→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 117 758 4643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074071
X-RAY DIFFRACTIONf_angle_d0.9825591
X-RAY DIFFRACTIONf_dihedral_angle_d13.9091440
X-RAY DIFFRACTIONf_chiral_restr0.092646
X-RAY DIFFRACTIONf_plane_restr0.008728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.27051830.26584177X-RAY DIFFRACTION93
1.31-1.330.3032420.26254294X-RAY DIFFRACTION99
1.33-1.340.31452380.2464368X-RAY DIFFRACTION100
1.34-1.360.26982170.23954439X-RAY DIFFRACTION100
1.36-1.380.2452170.23314320X-RAY DIFFRACTION100
1.38-1.40.23922140.22254425X-RAY DIFFRACTION100
1.4-1.420.22552440.21554341X-RAY DIFFRACTION100
1.42-1.440.23052230.21294424X-RAY DIFFRACTION100
1.44-1.460.2182290.19874359X-RAY DIFFRACTION100
1.46-1.490.19972320.2014369X-RAY DIFFRACTION100
1.49-1.510.22342530.19474360X-RAY DIFFRACTION100
1.51-1.540.23582360.19084365X-RAY DIFFRACTION100
1.54-1.570.2132290.18644408X-RAY DIFFRACTION100
1.57-1.60.19472190.18384393X-RAY DIFFRACTION100
1.6-1.640.18672200.17294381X-RAY DIFFRACTION100
1.64-1.670.192240.17814441X-RAY DIFFRACTION100
1.67-1.720.19092340.17724370X-RAY DIFFRACTION100
1.72-1.760.21822300.18244420X-RAY DIFFRACTION100
1.76-1.810.19452660.1734385X-RAY DIFFRACTION100
1.81-1.870.17932550.17464333X-RAY DIFFRACTION100
1.87-1.940.17962320.17524427X-RAY DIFFRACTION100
1.94-2.020.18412360.16964396X-RAY DIFFRACTION100
2.02-2.110.18062330.16084436X-RAY DIFFRACTION100
2.11-2.220.20282280.16214425X-RAY DIFFRACTION100
2.22-2.360.17352360.16484427X-RAY DIFFRACTION100
2.36-2.540.19362380.17094395X-RAY DIFFRACTION100
2.54-2.80.21082240.16964470X-RAY DIFFRACTION100
2.8-3.20.18862410.17264433X-RAY DIFFRACTION100
3.2-4.030.17412280.14714487X-RAY DIFFRACTION99
4.03-43.420.1472330.15184621X-RAY DIFFRACTION100

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