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- PDB-4b1m: CARBOHYDRATE BINDING MODULE CBM66 FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 4b1m
TitleCARBOHYDRATE BINDING MODULE CBM66 FROM BACILLUS SUBTILIS
ComponentsLEVANASE
KeywordsHYDROLASE / CBM66
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
levanbiose / Levanase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 2.1Dec 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
B: LEVANASE
C: LEVANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,14611
Polymers61,9313
Non-polymers1,2158
Water8,449469
1
A: LEVANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0324
Polymers20,6441
Non-polymers3883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LEVANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1054
Polymers20,6441
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LEVANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0093
Polymers20,6441
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.897, 36.909, 87.355
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LEVANASE


Mass: 20643.711 Da / Num. of mol.: 3 / Fragment: CARBOHYDRATE BINDING MODULE, 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) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05656, fructan beta-fructosidase
#2: Polysaccharide beta-D-fructofuranose-(2-6)-beta-D-fructofuranose / levanbiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: levanbiose
DescriptorTypeProgram
DFrufb2-6DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[ha122h-2b_2-5]/1-1/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(6+2)][b-D-Fruf]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 1.6-2.2 M AMMONIUM SULFATE, 1.4 - 2.4 M NACL, 5-6 MM LEVAN TRIOSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9784
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.1→43.67 Å / Num. obs: 158032 / % possible obs: 91.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 55.4

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Processing

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

4azz


Resolution: 1.1→87.35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.269 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED ATOMS WERE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.18121 7887 5 %RANDOM
Rwork0.15635 ---
obs0.15759 150129 91.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0.47 Å2
2---1.03 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.1→87.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 78 469 4355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024101
X-RAY DIFFRACTIONr_bond_other_d0.0010.022710
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9495594
X-RAY DIFFRACTIONr_angle_other_deg0.88536644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9645538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15625.076197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43115683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7951515
X-RAY DIFFRACTIONr_chiral_restr0.1980.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
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_restr2.99536808
X-RAY DIFFRACTIONr_sphericity_free28.8875181
X-RAY DIFFRACTIONr_sphericity_bonded10.39956995
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 305 -
Rwork0.323 5579 -
obs--46.39 %

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