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- PDB-1xxq: Structure of a mannose-specific jacalin-related lectin from Morus... -

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Basic information

Entry
Database: PDB / ID: 1xxq
TitleStructure of a mannose-specific jacalin-related lectin from Morus nigra
Componentsmannose-binding lectin
KeywordsSUGAR BINDING PROTEIN / tetrameric b-prism fold / jacalin-fold
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Mannose-binding lectin
Similarity search - Component
Biological speciesMorus nigra (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRabijns, A. / Barre, A. / Van Damme, E.J.M. / Peumans, W.J. / De Ranter, C.J. / Rouge, P.
CitationJournal: Febs J. / Year: 2005
Title: Structural analysis of the jacalin-related lectin MornigaM from the black mulberry (Morus nigra) in complex with mannose
Authors: Rabijns, A. / Barre, A. / Van Damme, E.J.M. / Peumans, W.J. / De Ranter, C.J. / Rouge, P.
History
DepositionNov 8, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mannose-binding lectin
B: mannose-binding lectin
C: mannose-binding lectin
D: mannose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,78912
Polymers68,1444
Non-polymers6458
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-45 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.740, 110.740, 159.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
mannose-binding lectin / mannose-specific jacalin-related lectin


Mass: 17035.980 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Morus nigra (plant) / References: UniProt: Q8LGR3
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 4.14 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulphate, imidazole buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 1999
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 100939 / Num. obs: 96741 / % possible obs: 90.6 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 20.84
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.96 / Num. unique all: 5072 / Rsym value: 0.16 / % possible all: 70.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 628569.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 4818 5 %RANDOM
Rwork0.19 ---
obs0.19 91450 94.8 %-
all-96741 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2074 Å2 / ksol: 0.370349 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å22.33 Å20 Å2
2--3.28 Å20 Å2
3----6.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→21.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 41 575 5256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.242 801 5.1 %
Rwork0.22 15057 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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