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- PDB-4i4r: BEL beta-trefoil apo crystal form 4 -

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Basic information

Entry
Database: PDB / ID: 4i4r
TitleBEL beta-trefoil apo crystal form 4
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 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
C: BEL-beta trefoil
D: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,61810
Polymers66,8864
Non-polymers7336
Water9,044502
1
A: BEL-beta trefoil
B: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9316
Polymers33,4432
Non-polymers4894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: BEL-beta trefoil
D: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6874
Polymers33,4432
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9663
Polymers16,7211
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9663
Polymers16,7211
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: 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
6
D: 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
Unit cell
Length a, b, c (Å)65.420, 70.030, 71.830
Angle α, β, γ (deg.)90.00, 106.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BEL-beta trefoil


Mass: 16721.391 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (fungus) / References: UniProt: R4GRU5*PLUS
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
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: 1.77→30 Å / Num. all: 59260 / Num. obs: 59260 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.2
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.2 / % possible all: 97

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I4P

4i4p


Resolution: 1.77→24.635 Å / SU ML: 0.54 / σ(F): 1.36 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 2997 5.06 %RANDOM
Rwork0.1764 ---
obs0.1786 59224 97.77 %-
all-59224 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.497 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2061 Å2-0 Å20.2489 Å2
2--0.2074 Å20 Å2
3----0.4135 Å2
Refinement stepCycle: LAST / Resolution: 1.77→24.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 48 502 5306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065008
X-RAY DIFFRACTIONf_angle_d1.066864
X-RAY DIFFRACTIONf_dihedral_angle_d11.0511820
X-RAY DIFFRACTIONf_chiral_restr0.081699
X-RAY DIFFRACTIONf_plane_restr0.005914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.7990.30461400.24732647X-RAY DIFFRACTION97
1.799-1.830.28121550.23532591X-RAY DIFFRACTION96
1.83-1.86330.28411390.21712653X-RAY DIFFRACTION97
1.8633-1.89910.24971600.20482624X-RAY DIFFRACTION97
1.8991-1.93790.26071210.18282659X-RAY DIFFRACTION97
1.9379-1.980.22761500.17682647X-RAY DIFFRACTION97
1.98-2.0260.23381430.17542631X-RAY DIFFRACTION98
2.026-2.07670.23721140.17072721X-RAY DIFFRACTION98
2.0767-2.13280.231280.16852679X-RAY DIFFRACTION98
2.1328-2.19550.24291490.17282654X-RAY DIFFRACTION98
2.1955-2.26640.20581380.1712661X-RAY DIFFRACTION98
2.2664-2.34730.2291540.17172687X-RAY DIFFRACTION98
2.3473-2.44120.20211460.17542642X-RAY DIFFRACTION98
2.4412-2.55220.21071300.17372704X-RAY DIFFRACTION98
2.5522-2.68660.25041310.17072712X-RAY DIFFRACTION98
2.6866-2.85470.23241650.18842667X-RAY DIFFRACTION98
2.8547-3.07470.21691530.18132695X-RAY DIFFRACTION99
3.0747-3.38340.21591350.18512705X-RAY DIFFRACTION99
3.3834-3.87140.20711470.16522742X-RAY DIFFRACTION99
3.8714-4.87140.16091430.14452720X-RAY DIFFRACTION99
4.8714-24.63720.22091560.18482786X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 5.6021 Å / Origin y: 17.0225 Å / Origin z: 17.857 Å
111213212223313233
T0.0118 Å20.0304 Å20.0047 Å2-0.0372 Å20.0186 Å2---0.034 Å2
L0.4384 °20.1257 °20.0764 °2-0.9954 °20.2456 °2--0.5699 °2
S-0.0102 Å °0.0046 Å °0.0216 Å °0.0174 Å °0.0444 Å °-0.0084 Å °-0.0285 Å °-0.086 Å °0.026 Å °
Refinement TLS groupSelection details: all

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