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- PDB-8szo: Canavalia villosa lectin in complex with alpha-methyl-mannoside -

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Basic information

Entry
Database: PDB / ID: 8szo
TitleCanavalia villosa lectin in complex with alpha-methyl-mannoside
ComponentsCanavalia villosa lectin
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding protein / Plant lectin / beta-sandwich / pro-inflammatory / PLANT PROTEIN
Function / homologymethyl alpha-D-mannopyranoside / :
Function and homology information
Biological speciesCanavalia villosa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCavada, B.S. / Lossio, C.F. / Pinto-Junior, V.R. / Osterne, V.J.S. / Oliveira, M.V. / Neco, A.H.B. / Nascimento, K.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: Int J Biol Macromol / Year: 2017
Title: Lectin from Canavalia villosa seeds: A glucose/mannose-specific protein and a new tool for inflammation studies.
Authors: Lossio, C.F. / Moreira, C.G. / Amorim, R.M.F. / Nobre, C.S. / Silva, M.T.L. / Neto, C.C. / Pinto-Junior, V.R. / Silva, I.B. / Campos, J. / Assreuy, A.M.S. / Cavada, B.S. / Nascimento, K.S.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Canavalia villosa lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0675
Polymers25,6851
Non-polymers3814
Water1,58588
1
A: Canavalia villosa lectin
hetero molecules

A: Canavalia villosa lectin
hetero molecules

A: Canavalia villosa lectin
hetero molecules

A: Canavalia villosa lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,26720
Polymers102,7424
Non-polymers1,52516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area10130 Å2
ΔGint-105 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.490, 84.440, 89.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Canavalia villosa lectin


Mass: 25685.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The residues S117, N118, S119 and T120 in the coordinate sequence are located in a loop region of the tertiary structure and were not detected due to lack of electron density on this ...Details: The residues S117, N118, S119 and T120 in the coordinate sequence are located in a loop region of the tertiary structure and were not detected due to lack of electron density on this specific region. This data deficiency is frequently observed in other ConA-like lectins structures solved by macromolecular crystallography. The sample sequence displays the full 237 amino acid of the protein.
Source: (natural) Canavalia villosa (plant)
#4: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 91 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.2
Details: PEG1000, potassium citrate phosphate, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.5→27.48 Å / Num. obs: 8301 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.056 / Rrim(I) all: 0.126 / Net I/σ(I): 8.9 / Num. measured all: 40674
Reflection shellResolution: 2.5→2.64 Å / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.433 / Num. measured all: 5399 / Num. unique obs: 1200 / CC1/2: 0.867 / Rpim(I) all: 0.224 / Rrim(I) all: 0.489 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→27.48 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 408 4.92 %
Rwork0.1813 --
obs0.1848 8295 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 21 88 1893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091847
X-RAY DIFFRACTIONf_angle_d0.9982518
X-RAY DIFFRACTIONf_dihedral_angle_d13.951650
X-RAY DIFFRACTIONf_chiral_restr0.057294
X-RAY DIFFRACTIONf_plane_restr0.009323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.640.29761200.22222604X-RAY DIFFRACTION100
2.64-3.60.2861390.20292602X-RAY DIFFRACTION100
3.6-27.480.2211490.15952681X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.6292 Å / Origin y: 14.4776 Å / Origin z: 11.3444 Å
111213212223313233
T0.2167 Å2-0.0522 Å2-0.0287 Å2-0.2166 Å2-0.0575 Å2--0.2272 Å2
L1.0932 °2-0.4264 °20.3622 °2-1.4682 °2-0.1789 °2--0.9354 °2
S0.0087 Å °-0.0128 Å °0.033 Å °0.1654 Å °0.0568 Å °-0.1773 Å °-0.0992 Å °0.0416 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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