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- PDB-1b2p: NATIVE MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUE... -

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Basic information

Entry
Database: PDB / ID: 1b2p
TitleNATIVE MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUEBELL) AT 1.7 ANGSTROMS RESOLUTION
ComponentsPROTEIN (LECTIN)
KeywordsSUGAR BINDING PROTEIN / MANNOSE-BINDING LECTIN / MONOCOT / AGLUTININ / BLUEBELL BULBS / PROTEIN- CARBOHYDRATE INTERACTIONS
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWood, S.D. / Wright, L.M. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. / Peumans, W.J. / Van Damme, E.J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of the native (unligated) mannose-specific bulb lectin from Scilla campanulata (bluebell) at 1.7 A resolution.
Authors: Wood, S.D. / Wright, L.M. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. / Peumans, W.J. / Van Damme, E.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallisation and Preliminary Structural Studies of Scilla Campanulata Lectin Complexed with Alpha (1-6)-Mannobiose
Authors: Wright, L.M. / Wood, S.D. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Scilla Campanulata Agglutinin Crystallized in Complex with the Trimannoside Alpha-D-Man-(1-6)-[Alpha-D-Man-(1-3)]-Alpha-D-Man
Authors: Wright, L.M. / Rizkallah, P.J. / Wood, S.D. / Reynolds, C.D.
#3: Journal: Protein Pept.Lett. / Year: 1997
Title: Crystallisation and Preliminary Crystallographic Analysis of Scilla Campanulata Lectin Complexed with Alpha-D-Mannose
Authors: Wright, L.M. / Wood, S.D. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Purification, Crystallisation and Preliminary X-Ray Analysis of a Mannose- Binding Lectin from Bluebell (Scilla Campanulata) Bulbs
Authors: Wright, L.M. / Wood, S.D. / Reynolds, C.D. / Rizkallah, P.J. / Peumans, W.J. / Vandamme, E.J.M. / Allen, A.K.
History
DepositionNov 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (LECTIN)
B: PROTEIN (LECTIN)


Theoretical massNumber of molelcules
Total (without water)26,4202
Polymers26,4202
Non-polymers00
Water4,414245
1
A: PROTEIN (LECTIN)
B: PROTEIN (LECTIN)

A: PROTEIN (LECTIN)
B: PROTEIN (LECTIN)


Theoretical massNumber of molelcules
Total (without water)52,8394
Polymers52,8394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-23 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.420, 92.950, 46.640
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 PROTEIN (LECTIN)


Mass: 13209.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: LOCATED IN THE BULBS OF SCILLA CAMPANULATA (BLUEBELL)
Source: (natural) Hyacinthoides hispanica (Spanish bluebell)
References: UniProt: Q9ZP49
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.78 Å3/Da / Density % sol: 56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.7
Details: HANGING-DROP VAPOUR-DIFFUSION METHOD WELL: 70% SATURATED AMMONIUM SULPHATE, PH 4.7 DROP: 5.5 MG/ML PROTEIN, 10MM DAP, 600MM PHOSPHATE BUFFERED SALINE, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
15.5 MG/ML PROTEIN11
210MM DAP11
3600MM PHOSPHATE BUFFERED SALINE11
470% SATURATED AMMONIUM SULPHATE, PH 4.712
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2600 mMphosphate1drop
370 %satammonium sulfate1reservoir
41

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 13, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 33837 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.039 / Rsym value: 0.1
Reflection shellHighest resolution: 1.7 Å
Reflection
*PLUS
Num. measured all: 161054
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4(ROTAVATA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNA

1gna


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.225 / Details: X-PLOR WAS USED INITIALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1709 5 %RANDOM
Rwork0.186 ---
obs-33837 98.5 %-
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 0 245 2109
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d1.709
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg29.278
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg0.769

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