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- PDB-1xd6: Crystal structures of novel monomeric monocot mannose-binding lec... -

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Basic information

Entry
Database: PDB / ID: 1xd6
TitleCrystal structures of novel monomeric monocot mannose-binding lectins from Gastrodia elata
Componentsgastrodianin-4
KeywordsANTIFUNGAL PROTEIN / monocot mannose-binding lectin / monomer / homogeneous beta-sheet
Function / homology
Function and homology information


response to other organism
Similarity search - Function
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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesGastrodia elata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, W. / Yang, N. / Wang, M. / Huang, R.H. / Hu, Z. / Wang, D.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Mechanism Governing the Quaternary Organization of Monocot Mannose-binding Lectin Revealed by the Novel Monomeric Structure of an Orchid Lectin
Authors: Liu, W. / Yang, N. / Ding, J. / Huang, R.H. / Hu, Z. / Wang, D.C.
History
DepositionSep 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: gastrodianin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3462
Polymers12,2501
Non-polymers961
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.070, 97.480, 36.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein gastrodianin-4


Mass: 12249.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gastrodia elata (plant) / Tissue: corms / References: UniProt: Q1M0Y9
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, MPD, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 0.98 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 15, 2001
RadiationMonochromator: Silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→18.93 Å / Num. all: 9647 / Num. obs: 9217 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.067 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.07 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.93 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 4.53 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.182 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23829 948 10.4 %RANDOM
Rwork0.19856 ---
all0.218 9092 --
obs0.20267 8143 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.504 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2---0.8 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2→18.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 5 43 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9291172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02676
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2329
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.460.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.81.5540
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4952853
X-RAY DIFFRACTIONr_scbond_it1.9593325
X-RAY DIFFRACTIONr_scangle_it3.1374.5319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 65
Rwork0.246 532

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