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- PDB-4i4o: BEL beta-trefoil apo crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 4i4o
TitleBEL beta-trefoil apo crystal form 1
ComponentsBEL beta-trefoil
KeywordsSUGAR BINDING PROTEIN / lectin / galactose / 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 / MOLECULAR REPLACEMENT / Resolution: 1.12 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,46013
Polymers33,4432
Non-polymers1,01711
Water6,846380
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)17,2787
Polymers16,7211
Non-polymers5576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: BEL beta-trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1826
Polymers16,7211
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.530, 66.830, 63.940
Angle α, β, γ (deg.)90.00, 96.10, 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.: 2 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (king bolete) / References: UniProt: R4GRU5*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 1.5 M ammonium sulfate, 10% glycerol, 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: ID29 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2011
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.12→63.6 Å / Num. all: 110718 / Num. obs: 103662 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 6.9 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 18
Reflection shellResolution: 1.12→1.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 8.8 / % possible all: 81.6

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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: 1.12→29.579 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 13.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1597 5191 5.01 %RANDOM
Rwork0.1509 ---
obs0.1513 103652 93.62 %-
all-103696 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.401 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0006 Å2-0 Å20.0184 Å2
2---0.011 Å2-0 Å2
3---0.0116 Å2
Refinement stepCycle: LAST / Resolution: 1.12→29.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 65 380 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052520
X-RAY DIFFRACTIONf_angle_d1.1463433
X-RAY DIFFRACTIONf_dihedral_angle_d11.811907
X-RAY DIFFRACTIONf_chiral_restr0.083345
X-RAY DIFFRACTIONf_plane_restr0.007453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.13270.16731110.16132418X-RAY DIFFRACTION69
1.1327-1.14610.15711300.1512719X-RAY DIFFRACTION77
1.1461-1.160.14361600.1462927X-RAY DIFFRACTION84
1.16-1.17470.15391860.14173120X-RAY DIFFRACTION90
1.1747-1.19020.15771640.14143336X-RAY DIFFRACTION95
1.1902-1.20650.14341990.14423285X-RAY DIFFRACTION95
1.2065-1.22370.161640.13943330X-RAY DIFFRACTION95
1.2237-1.2420.15241920.14133285X-RAY DIFFRACTION95
1.242-1.26140.16071910.14193302X-RAY DIFFRACTION94
1.2614-1.28210.18241800.14273179X-RAY DIFFRACTION91
1.2821-1.30420.14431700.14163247X-RAY DIFFRACTION94
1.3042-1.32790.15931870.14023384X-RAY DIFFRACTION96
1.3279-1.35340.15711850.14533309X-RAY DIFFRACTION96
1.3534-1.38110.15511610.14353409X-RAY DIFFRACTION96
1.3811-1.41110.14722050.13973283X-RAY DIFFRACTION96
1.4111-1.44390.1391570.13943361X-RAY DIFFRACTION95
1.4439-1.480.15761670.1383241X-RAY DIFFRACTION93
1.48-1.52010.13791720.13423381X-RAY DIFFRACTION96
1.5201-1.56480.14021650.12643399X-RAY DIFFRACTION96
1.5648-1.61530.14761810.13023365X-RAY DIFFRACTION97
1.6153-1.6730.13481800.13563439X-RAY DIFFRACTION98
1.673-1.740.15951550.14143415X-RAY DIFFRACTION96
1.74-1.81920.15071980.14493253X-RAY DIFFRACTION93
1.8192-1.91510.15341800.14443432X-RAY DIFFRACTION98
1.9151-2.0350.17161580.15433465X-RAY DIFFRACTION98
2.035-2.19210.15491600.15443481X-RAY DIFFRACTION99
2.1921-2.41260.16931710.15793440X-RAY DIFFRACTION97
2.4126-2.76150.16081860.17083338X-RAY DIFFRACTION95
2.7615-3.47830.18831820.16933476X-RAY DIFFRACTION98
3.4783-29.58890.16261940.15963442X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 2.2216 Å / Origin y: 5.767 Å / Origin z: 19.099 Å
111213212223313233
T0.0262 Å2-0.0013 Å20.0009 Å2-0.0259 Å20.0033 Å2--0.0424 Å2
L0.2398 °2-0.008 °2-0.0323 °2-0.2532 °20.2294 °2--0.828 °2
S-0.0045 Å °-0.0153 Å °-0.0043 Å °-0.0008 Å °0.012 Å °0.0057 Å °0.0147 Å °0.0193 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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