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- PDB-4jjj: The structure of T. fusca GH48 D224N mutant -

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Basic information

Entry
Database: PDB / ID: 4jjj
TitleThe structure of T. fusca GH48 D224N mutant
ComponentsCellulose 1,4-beta-cellobiosidase
KeywordsHYDROLASE / GH48 / (a/a)6 / cellobiohydrolase
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Cellulose binding domain / Carbohydrate-binding type-2 domain ...Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / PKD domain superfamily / Glycosyltransferase - #10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Few Secondary Structures / Irregular / Immunoglobulin-like fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-cellobiose / beta-cellohexaose / alpha-cellobiose / ACETATE ION / : / Cellulose 1,4-beta-cellobiosidase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Biotechnol.Bioeng. / Year: 2014
Title: Cel48A from Thermobifida fusca: structure and site directed mutagenesis of key residues.
Authors: Kostylev, M. / Alahuhta, M. / Chen, M. / Brunecky, R. / Himmel, M.E. / Lunin, V.V. / Brady, J. / Wilson, D.B.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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: Cellulose 1,4-beta-cellobiosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,44139
Polymers71,7591
Non-polymers3,68238
Water20,4651136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.458, 88.494, 66.753
Angle α, β, γ (deg.)90.00, 113.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cellulose 1,4-beta-cellobiosidase


Mass: 71759.320 Da / Num. of mol.: 1 / Fragment: UNP residues 343-984 / Mutation: D224N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: Tfu_1959 / Production host: Escherichia coli (E. coli)
References: UniProt: Q47NH7, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 3 types, 3 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
#4: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellohexaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 1171 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#8: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1136 / 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate trihydrate pH 6.5, 18% (w/v) PEG 8000 and 20 mM zinc acetate dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 30, 2012
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 78727 / Num. obs: 78727 / % possible obs: 99.4 % / Redundancy: 7.93 % / Rsym value: 0.0886 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.32 % / Mean I/σ(I) obs: 3.81 / Num. unique all: 12722 / Rsym value: 0.2506 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
REFMAC5.7.0032refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FUS

4fus


Resolution: 1.6→25 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.343 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16379 4001 5.1 %RANDOM
Rwork0.12133 ---
obs0.12351 74622 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.472 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5047 0 157 1136 6340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.025768
X-RAY DIFFRACTIONr_bond_other_d0.0060.024898
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.9417961
X-RAY DIFFRACTIONr_angle_other_deg1.3113.00211376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86324.966294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71615800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4821519
X-RAY DIFFRACTIONr_chiral_restr0.1410.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216860
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021417
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 298 -
Rwork0.19 5239 -
obs--94.97 %

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