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- PDB-4b1l: CARBOHYDRATE BINDING MODULE CBM66 FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 4b1l
TitleCARBOHYDRATE BINDING MODULE CBM66 FROM BACILLUS SUBTILIS
ComponentsLEVANASE
KeywordsHYDROLASE / LEVAN
Function / homology
Function and homology information


fructan beta-fructosidase / fructan beta-fructosidase activity / sucrose alpha-glucosidase activity / sucrose catabolic process / extracellular region / cytoplasm
Similarity search - Function
3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain ...3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-fructofuranose / Levanase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCuskin, F. / Flint, J.E. / Morland, C. / Basle, A. / Henrissat, B. / Countinho, P.M. / Strazzulli, A. / Solzehinkin, A. / Davies, G.J. / Gilbert, H.J. / Gloster, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: How Nature Can Exploit Nonspecific Catalytic and Carbohydrate Binding Modules to Create Enzymatic Specificity
Authors: Cuskin, F. / Flint, J.E. / Gloster, T.M. / Morland, C. / Basle, A. / Henrissat, B. / Coutinho, P.M. / Strazzulli, A. / Solovyova, A.S. / Davies, G.J. / Gilbert, H.J.
History
DepositionJul 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEVANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4513
Polymers18,2481
Non-polymers2032
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.616, 38.616, 162.391
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LEVANASE / BETA-D-FRUCTOFURANOSIDASE / EXO-BETA-D-FRUCTOSIDASE / EXO-LEVANASE


Mass: 18248.121 Da / Num. of mol.: 1 / Fragment: RESIDUES 515-677
Source method: isolated from a genetically manipulated source
Details: CARBOHYDRATE BINDING MODULE WAS PREDICTED TO COMPRISE RESIDUES 515-677 OF THE FULL LENGTH PROTEIN.
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 1423 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05656, fructan beta-fructosidase
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFRUCTOSE (FRU): THE PROTEIN WAS CO-CRYSTALLISED WITH 5-6 MM OF LEVAN BIOSE BUT ONLY THE CONTAMINANT ...FRUCTOSE (FRU): THE PROTEIN WAS CO-CRYSTALLISED WITH 5-6 MM OF LEVAN BIOSE BUT ONLY THE CONTAMINANT MONOMER FRUCTOSE COULD BE SEEN IN THE STRUCTURE.
Sequence detailsRESIDUES 515-677 OF THE FULL LENGTH PROTEIN WERE CLONED IN PET16B VECTOR. THE PROTEIN WAS DIGESTED ...RESIDUES 515-677 OF THE FULL LENGTH PROTEIN WERE CLONED IN PET16B VECTOR. THE PROTEIN WAS DIGESTED WITH FACTOR XA LEAVING ONLY HM RESIDUES IN N-TERMINAL OF THE TARGET SEQUENCE FOR CRYSTALLISATION.

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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: 1.7 Å3/Da / Density % sol: 27.5 % / Description: NONE
Crystal growDetails: 25% (W/V) PEG 1500, 100MM MMT BUFFER, 5-6 MM LEVAN BIOSE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Nov 17, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.65→40.6 Å / Num. obs: 17659 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AZZ

4azz


Resolution: 1.65→54.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.718 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED ATOMS WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25591 899 5.1 %RANDOM
Rwork0.1761 ---
obs0.17998 16699 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.258 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.65→54.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 13 56 1329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9341753
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0265161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6142564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80615213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.754155
X-RAY DIFFRACTIONr_chiral_restr0.1040.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02990
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.43231298
X-RAY DIFFRACTIONr_sphericity_free15.496525
X-RAY DIFFRACTIONr_sphericity_bonded12.62651304
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 52 -
Rwork0.192 928 -
obs--82.63 %

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