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- PDB-1g9j: X-TAL STRUCTURE OF THE MUTANT E44Q OF THE CELLULASE CEL48F IN COM... -

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Entry
Database: PDB / ID: 1g9j
TitleX-TAL STRUCTURE OF THE MUTANT E44Q OF THE CELLULASE CEL48F IN COMPLEX WITH A THIOOLIGOSACCHARIDE
ComponentsCELLULASE CEL48F
KeywordsHYDROLASE / alpha-alpha-6-barrel / cellulase / thiooligosaccharide
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
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 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin 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 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / EF-hand calcium-binding domain. / Few Secondary Structures / Irregular / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesClostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsParsiegla, G. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structures of mutants of cellulase Cel48F of Clostridium cellulolyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action
Authors: Parsiegla, G. / Reverbel, C. / Tardif, C. / Driguez, H. / Haser, R.
#1: Journal: Biochemistry / Year: 2000
Title: Crystal structures of the cellulase Cel48F in complex with inhibitors and substrates give insights into its processive action.
Authors: Parsiegla, G. / Reverbel-Leroy, C. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
#2: Journal: Embo J. / Year: 1998
Title: The crystal structure of the processive endocellulase CelF of Clostridium cellullolyticum in complex with a thiooligosaccharide inhibitor at 2.0 resolution.
Authors: Parsiegla, G. / Juy, M. / Reverbel-Leroy, C. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
History
DepositionNov 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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 / _chem_comp.name / _chem_comp.type / _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_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 / _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 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULASE CEL48F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3645
Polymers70,8691
Non-polymers1,4954
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.480, 84.720, 121.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELLULASE CEL48F


Mass: 70868.891 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE / Mutation: E44Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37698, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta- ...beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1379.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/1,8,7/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1/a4-b1*S*_b4-c1_c4-d1*S*_d4-e1_e4-f1*S*_f4-g1_g4-h1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, PEG 4000, CaCl2, thiooligosaccharide IG12, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reverbel-Leroy, C., (1997) Acta Crystallogr., D.54, 114.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
22 mMIG41drop
30.5 M1reservoiror 0.3MNaCl
4PEG40001drop

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FU581 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2000 / Details: Osmic confocal mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 50753 / Num. obs: 45078 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.7 / Num. unique all: 12065 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 1.9→49.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2100897.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2585 5.1 %OTHER
Rwork0.182 ---
obs0.182 50697 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.67 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---2.6 Å20 Å2
3---2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5101 0 92 375 5568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.521.5
X-RAY DIFFRACTIONc_mcangle_it0.892
X-RAY DIFFRACTIONc_scbond_it0.932
X-RAY DIFFRACTIONc_scangle_it1.42.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 419 5 %
Rwork0.255 7880 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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