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- PDB-1uln: Crystal Structure of Pokeweed Lectin-D1 -

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Basic information

Entry
Database: PDB / ID: 1uln
TitleCrystal Structure of Pokeweed Lectin-D1
Componentslectin-D
KeywordsSUGAR BINDING PROTEIN / lectin / chitin-binding domain
Function / homology
Function and homology information


chitin binding / positive regulation of cell division / positive regulation of mitotic nuclear division / carbohydrate binding
Similarity search - Function
Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFujii, T. / Hayashida, M. / Hamasu, M. / Ishiguro, M. / Hata, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structures of two lectins from the roots of pokeweed (Phytolacca americana).
Authors: Fujii, T. / Hayashida, M. / Hamasu, M. / Ishiguro, M. / Hata, Y.
History
DepositionSep 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lectin-D


Theoretical massNumber of molelcules
Total (without water)9,3261
Polymers9,3261
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.664, 49.012, 29.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein lectin-D / lectin-D1


Mass: 9326.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytolacca americana (American pokeweed) / Tissue: roots / References: UniProt: P83790
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.69 Å3/Da / Density % sol: 26.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, 0.2M calcium acetate, 0.1M sodium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 9068 / Num. obs: 9068 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.4 Å2
Reflection shellResolution: 1.65→1.75 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→18.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 608320.81 / 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
Rfree0.205 951 10.5 %RANDOM
Rwork0.172 ---
all0.175 9034 --
obs0.172 9034 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.04 Å2 / ksol: 0.378846 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.65→18.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 0 133 755
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 164 11 %
Rwork0.176 1322 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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