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- PDB-1dlp: STRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN ... -

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Entry
Database: PDB / ID: 1dlp
TitleSTRUCTURAL CHARACTERIZATION OF THE NATIVE FETUIN-BINDING PROTEIN SCILLA CAMPANULATA AGGLUTININ (SCAFET): A NOVEL TWO-DOMAIN LECTIN
ComponentsLECTIN SCAFET PRECURSOR
KeywordsSUGAR BINDING PROTEIN / TWO-DOMAIN LECTIN / BETA PRISM II FOLD / NATIVE
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 speciesHyacinthoides hispanica (Spanish bluebell)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsWright, L.M. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. / VanDamme, E.J.M. / Donovan, M.J. / Peumans, W.J.
Citation
Journal: FEBS Lett. / Year: 2000
Title: Structural characterisation of the native fetuin-binding protein Scilla campanulata agglutinin: a novel two-domain lectin.
Authors: Wright, L.M. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. / Van Damme, E.J. / Donovan, M.J. / Peumans, W.J.
#1: Journal: Protein Pept.Lett. / Year: 1999
Title: Purification and Crystallisation of a Novel Two-Domain Lectin from Scilla Campanulata
Authors: Wright, L.M. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. / Peumans, W.J. / Van Damme, E. / Donovan, M.J.
#2: Journal: Biochem.J. / Year: 1999
Title: Isolation, characterization, molecular cloning and molecular modelling of two lectins of different specificities from bluebell (Scilla campanulata) bulbs
Authors: Wright, L.M. / Van Damme, E.J. / Barre, A. / Allen, A.K. / Van Leuven, F. / Reynolds, C.D. / Rouge, P. / Peumans, W.J.
History
DepositionDec 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LECTIN SCAFET PRECURSOR
B: LECTIN SCAFET PRECURSOR
C: LECTIN SCAFET PRECURSOR
D: LECTIN SCAFET PRECURSOR
E: LECTIN SCAFET PRECURSOR
F: LECTIN SCAFET PRECURSOR


Theoretical massNumber of molelcules
Total (without water)153,2726
Polymers153,2726
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)277.940, 164.100, 53.600
Angle α, β, γ (deg.)90.00, 95.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LECTIN SCAFET PRECURSOR


Mass: 25545.377 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: PROTEIN WAS EXTRACTED FROM THE BULBS OF THIS PLANT
Source: (natural) Hyacinthoides hispanica (Spanish bluebell)
References: UniProt: Q9ZP48
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 70% Ammonium sulphate, Acetic Acid buffer, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 70 %sat / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 34139 / % possible obs: 95.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 3.3→20 Å / Stereochemistry target values: Engh & Huber / Details: Used weighted maximum likelihood procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1707 -Random 5%
Rwork0.189 ---
obs-34139 95.3 %-
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10364 0 0 67 10431

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