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- PDB-1fbo: Crystal structure of the cellulase CEL48F from C. cellulolyticum ... -

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Basic information

Entry
Database: PDB / ID: 1fbo
TitleCrystal structure of the cellulase CEL48F from C. cellulolyticum in complex with cellobiitol
ComponentsENDO-1,4-BETA-GLUCANASE F
KeywordsHYDROLASE / Cellulase / Protein-Cellobiitol Complex
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: 2.3 Å
AuthorsParsiegla, G. / Reverbel-Leroy, C. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
Citation
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.
#1: Journal: Embo J. / Year: 1998
Title: The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 A
Authors: Parsiegla, G. / Juy, M. / Reverbel-Leroy, C. / Tardif, C. / Belaich, J.P. / Driguez, H. / Haser, R.
History
DepositionJul 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-BETA-GLUCANASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2523
Polymers70,8701
Non-polymers3822
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.460, 84.820, 121.750
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 ENDO-1,4-BETA-GLUCANASE F / CELLULASE CEL48F / CELLULASE F / EGCCF


Mass: 70869.875 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Plasmid: PETFC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P37698, cellulase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-D-glucose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[o2122h][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][b-D-Glcp]{}}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


Mass: 18.015 Da / Num. of mol.: 263 / 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: 45.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, HEPES, Calcium chloride, Cellobiitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
24 mMsubstrate/inhibitor 1drop
32 mMIG41drop
40.5 M1reservoiror 0.3MNaCl

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.36 Å / Num. all: 27615 / Num. obs: 23964 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.418 / Num. unique all: 1458 / % possible all: 90.3
Reflection shell
*PLUS
% possible obs: 90.3 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
X-PLORmodel building
CNS0.9refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2.3→29.32 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1418 -based on 1fce
Rwork0.166 ---
all-27579 --
obs-27579 95.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5015 0 24 263 5302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_torsion_deg21.9
X-RAY DIFFRACTIONc_torsion_impr_deg0.76

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