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- PDB-4i4p: BEL beta-trefoil apo crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 4i4p
TitleBEL beta-trefoil apo crystal form 2
ComponentsBEL-beta trefoil
KeywordsSUGAR BINDING PROTEIN / lectin / fruiting bodies
Function / homologyRicin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / BEL-beta trefoil
Function and homology information
Biological speciesBoletus edulis (king bolete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.279 Å
AuthorsBovi, M. / Cenci, L. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Civiero, L. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
CitationJournal: Glycobiology / Year: 2013
Title: BEL {beta}-trefoil: A novel lectin with antineoplastic properties in king bolete (Boletus edulis) mushrooms.
Authors: Bovi, M. / Cenci, L. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Civiero, L. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: BEL-beta trefoil
B: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9316
Polymers33,4432
Non-polymers4894
Water7,422412
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8442
Polymers16,7211
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0884
Polymers16,7211
Non-polymers3663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.580, 66.580, 105.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BEL-beta trefoil


Mass: 16721.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (king bolete) / References: UniProt: R4GRU5*PLUS
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M magnesium chloride, 25% PEG4000, 0.2 M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.279→30 Å / Num. all: 70848 / Num. obs: 70848 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.8
Reflection shellResolution: 1.279→1.35 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 6.1 / % possible all: 86.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.279→19.845 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 15.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 3564 5.03 %RANDOM
Rwork0.1666 ---
obs0.1676 70792 93.01 %-
all-70848 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.565 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1351 Å2-0 Å20 Å2
2---0.1521 Å2-0 Å2
3---0.017 Å2
Refinement stepCycle: LAST / Resolution: 1.279→19.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 32 412 2822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062490
X-RAY DIFFRACTIONf_angle_d1.1283406
X-RAY DIFFRACTIONf_dihedral_angle_d10.674900
X-RAY DIFFRACTIONf_chiral_restr0.084344
X-RAY DIFFRACTIONf_plane_restr0.006452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.279-1.29650.2281180.20182246X-RAY DIFFRACTION78
1.2965-1.3150.24031220.20912532X-RAY DIFFRACTION88
1.315-1.33470.25411310.19652511X-RAY DIFFRACTION88
1.3347-1.35550.20331440.17972512X-RAY DIFFRACTION89
1.3555-1.37770.19991330.17542559X-RAY DIFFRACTION89
1.3777-1.40150.20891370.17192524X-RAY DIFFRACTION89
1.4015-1.4270.18651180.16452562X-RAY DIFFRACTION89
1.427-1.45440.2241330.15742561X-RAY DIFFRACTION90
1.4544-1.48410.1751350.1592565X-RAY DIFFRACTION89
1.4841-1.51630.17941390.14932582X-RAY DIFFRACTION91
1.5163-1.55160.17391170.15092584X-RAY DIFFRACTION90
1.5516-1.59040.18091450.14982621X-RAY DIFFRACTION91
1.5904-1.63340.16851530.15572636X-RAY DIFFRACTION93
1.6334-1.68140.1731330.15462724X-RAY DIFFRACTION94
1.6814-1.73560.16081680.15622719X-RAY DIFFRACTION95
1.7356-1.79760.16771420.15512767X-RAY DIFFRACTION96
1.7976-1.86960.18021530.15722803X-RAY DIFFRACTION97
1.8696-1.95460.1611430.16132810X-RAY DIFFRACTION98
1.9546-2.05750.17971670.16012832X-RAY DIFFRACTION98
2.0575-2.18630.19971580.16162876X-RAY DIFFRACTION98
2.1863-2.35480.20541570.16962855X-RAY DIFFRACTION99
2.3548-2.59140.19471420.17092908X-RAY DIFFRACTION99
2.5914-2.96530.17691570.18552927X-RAY DIFFRACTION99
2.9653-3.73180.18711650.16492940X-RAY DIFFRACTION99
3.7318-19.84740.16991540.16973072X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 10.3432 Å / Origin y: 27.3078 Å / Origin z: 12.8796 Å
111213212223313233
T0.0197 Å20.005 Å20.0041 Å2-0.0621 Å20.0058 Å2--0.0311 Å2
L0.3305 °20.2327 °20.0159 °2-1.3576 °20.0304 °2--0.3955 °2
S-0.0123 Å °0.0009 Å °-0.0006 Å °-0.0213 Å °0.0087 Å °0.0033 Å °-0.0187 Å °0.0246 Å °0.0036 Å °
Refinement TLS groupSelection details: all

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