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- PDB-8ux7: Dioclea megacarpa lectin (DmegA) complexed with X-Man -

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Basic information

Entry
Database: PDB / ID: 8ux7
TitleDioclea megacarpa lectin (DmegA) complexed with X-Man
ComponentsDioclea megacarpa lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Legume / ConA-like / Dioclea
Function / homology: / : / Chem-XMM
Function and homology information
Biological speciesMacropsychanthus megacarpus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOliveira, M.V. / De Sloover, G. / Osterne, V.J.S. / Pinto-Junior, V.R. / Sacramento-Neto, J.C. / Van Damme, E.J.M. / Nascimento, K.S. / Cavada, B.S.
Funding support Brazil, Belgium, 3items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Research Foundation - Flanders (FWO)12T4622N Belgium
CitationJournal: To Be Published
Title: Dioclea megacarpa lectin (DmegA) complexed with X-Man
Authors: Oliveira, M.V. / De Sloover, G. / Osterne, V.J.S. / Pinto-Junior, V.R. / Sacramento-Neto, J.C. / Van Damme, E.J.M. / Nascimento, K.S. / Cavada, B.S.
History
DepositionNov 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dioclea megacarpa lectin
B: Dioclea megacarpa lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26310
Polymers51,1252
Non-polymers1,1388
Water1,53185
1
A: Dioclea megacarpa lectin
B: Dioclea megacarpa lectin
hetero molecules

A: Dioclea megacarpa lectin
B: Dioclea megacarpa lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,52620
Polymers102,2494
Non-polymers2,27716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10130 Å2
ΔGint-108 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.350, 109.414, 126.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Dioclea megacarpa lectin


Mass: 25562.268 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Macropsychanthus megacarpus (plant)
#4: Sugar ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15BrClNO6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 91 molecules

#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5, 0.5% PEGME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 2.2→46.661 Å / Num. obs: 31790 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Χ2: 1 / Net I/σ(I): 21.6
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.148 / Num. measured all: 36823 / Num. unique obs: 2714 / CC1/2: 0.853 / Rpim(I) all: 0.322 / Rrim(I) all: 1.193 / Χ2: 0.99 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
MOSFLM7.4.0data reduction
SCALA3.3.21data scaling
MOLREP11phasing
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.661 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.211 / SU ML: 0.167 / Cross valid method: FREE R-VALUE / ESU R: 0.22 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2483 1593 5.017 %
Rwork0.2006 30159 -
all0.203 --
obs-31752 99.852 %
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: 50.893 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.007 Å20 Å2
3---0.013 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 57 85 3690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123685
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163360
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.6495023
X-RAY DIFFRACTIONr_angle_other_deg0.4981.5787768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4965460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.591518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95810568
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.56610150
X-RAY DIFFRACTIONr_chiral_restr0.0630.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
X-RAY DIFFRACTIONr_nbd_refined0.2220.2697
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.23135
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21840
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2143
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.213
X-RAY DIFFRACTIONr_nbd_other0.1480.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.222
X-RAY DIFFRACTIONr_mcbond_it4.3725.051852
X-RAY DIFFRACTIONr_mcbond_other4.3685.051852
X-RAY DIFFRACTIONr_mcangle_it6.1349.0482308
X-RAY DIFFRACTIONr_mcangle_other6.1359.0492309
X-RAY DIFFRACTIONr_scbond_it4.9565.4471833
X-RAY DIFFRACTIONr_scbond_other4.9555.4481834
X-RAY DIFFRACTIONr_scangle_it7.229.7862715
X-RAY DIFFRACTIONr_scangle_other7.2199.7862716
X-RAY DIFFRACTIONr_lrange_it9.75648.8714043
X-RAY DIFFRACTIONr_lrange_other9.74548.8394041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.4021260.3562205X-RAY DIFFRACTION99.9571
2.257-2.3190.3331240.3272111X-RAY DIFFRACTION99.9106
2.319-2.3860.3291100.2912081X-RAY DIFFRACTION99.9544
2.386-2.4590.3361100.2912033X-RAY DIFFRACTION100
2.459-2.5390.321890.2831962X-RAY DIFFRACTION99.9513
2.539-2.6280.3181000.2811948X-RAY DIFFRACTION99.9024
2.628-2.7270.366970.2741809X-RAY DIFFRACTION100
2.727-2.8380.3221000.2711774X-RAY DIFFRACTION99.9467
2.838-2.9640.274930.231707X-RAY DIFFRACTION99.9445
2.964-3.1080.292810.2111621X-RAY DIFFRACTION99.7071
3.108-3.2750.329840.2271563X-RAY DIFFRACTION99.637
3.275-3.4730.239780.2141450X-RAY DIFFRACTION99.6089
3.473-3.7110.256710.1931404X-RAY DIFFRACTION99.797
3.711-4.0060.224650.1821296X-RAY DIFFRACTION99.9266
4.006-4.3850.165620.1631217X-RAY DIFFRACTION99.766
4.385-4.8980.2530.1191091X-RAY DIFFRACTION100
4.898-5.6450.159530.137976X-RAY DIFFRACTION100
5.645-6.8880.238460.162838X-RAY DIFFRACTION100
6.888-9.6370.158330.132665X-RAY DIFFRACTION100
9.637-46.6610.179180.202408X-RAY DIFFRACTION97.931

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