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- PDB-2qno: Crystal Structure of the Mutant E55Q of the Cellulase CEL48F in C... -

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Basic information

Entry
Database: PDB / ID: 2qno
TitleCrystal Structure of the Mutant E55Q of the Cellulase CEL48F in Complex with a Thio-Oligosaccharide
ComponentsEndoglucanase F
KeywordsHYDROLASE / Cellulase / Thio-oligosaccharide complex / Inactive mutant / GH family 48 / alpha-alpha-six barrel / Carbohydrate metabolism / Cellulose degradation / Glycosidase / Polysaccharide degradation
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsParsiegla, G. / Haser, R.
CitationJournal: 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.
History
DepositionJul 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 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 / diffrn_source / 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_conn_type / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 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 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4673
Polymers70,8691
Non-polymers1,5982
Water7,422412
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.240, 84.720, 121.740
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 Endoglucanase F / Endo-1 / 4-beta-glucanase F / Cellulase F / EGCCF


Mass: 70868.891 Da / Num. of mol.: 1 / Fragment: Catalytic module / Mutation: E55Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Gene: celCCF / Plasmid: pETF55 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37698, cellulase
#2: Polysaccharide 4-thio-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-beta- ...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-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1557.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,9,8/[a2122h-1b_1-5][a2122h-1b_1-5_4*S]/1-1-1-1-1-1-1-1-2/a4-b1*S*_b4-c1_c4-d1*S*_d4-e1_e4-f1*S*_f4-g1_g4-h1*S*_h4-i1WURCSPDB2Glycan 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]{[(4+1)][b-D-Glcp4SH]{}}}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Sodium-HEPES, 8 % w/v PEG 4000, 20 mM Calcium chloride, 8 mM Thio-oligosaccharide IG10, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→29.303 Å / Num. all: 41553 / Num. obs: 41188 / % possible obs: 95.2 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.078 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3 / Num. unique all: 2761 / Rsym value: 0.1999 / % possible all: 95.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FCE

1fce


Resolution: 2→29.303 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.903 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2096 5.1 %RANDOM
Rwork0.137 ---
obs0.14 41164 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2→29.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 101 412 5584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225350
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.947293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84924.402259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19115792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2381519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024184
X-RAY DIFFRACTIONr_nbd_refined0.1930.22423
X-RAY DIFFRACTIONr_nbtor_refined0.310.23720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2369
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.29
X-RAY DIFFRACTIONr_mcbond_it0.9461.53238
X-RAY DIFFRACTIONr_mcangle_it1.4725077
X-RAY DIFFRACTIONr_scbond_it2.33132528
X-RAY DIFFRACTIONr_scangle_it3.4064.52216
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 133 -
Rwork0.159 2627 -
obs-2760 87.04 %

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