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- PDB-1egn: CELLOBIOHYDROLASE CEL7A (E223S, A224H, L225V, T226A, D262G) MUTANT -

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Basic information

Entry
Database: PDB / ID: 1egn
TitleCELLOBIOHYDROLASE CEL7A (E223S, A224H, L225V, T226A, D262G) MUTANT
Components1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE CEL7A
KeywordsHYDROLASE / GLYCOSIDASE / CELLULASE / CELLULOSE DEGRADATION / GLYCOPROTEIN / GLYCOSYLATED PROTEIN / PH-MUTANT
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region
Similarity search - Function
1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. ...1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsStahlberg, J. / Harris, M. / Jones, T.A.
Citation
Journal: Biochem.J. / Year: 2001
Title: Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and its E223S/ A224H/L225V/T226A/D262G mutant.
Authors: Becker, D. / Braet, C. / Brumer III, H. / Claeyssens, M. / Divne, C. / Fagerstrom, B.R. / Harris, M. / Jones, T.A. / Kleywegt, G.J. / Koivula, A. / Mahdi, S. / Piens, K. / Sinnott, M.L. / ...Authors: Becker, D. / Braet, C. / Brumer III, H. / Claeyssens, M. / Divne, C. / Fagerstrom, B.R. / Harris, M. / Jones, T.A. / Kleywegt, G.J. / Koivula, A. / Mahdi, S. / Piens, K. / Sinnott, M.L. / Stahlberg, J. / Teeri, T.T. / Underwood, M. / Wohlfahrt, G.
#1: Journal: Science / Year: 1994
Title: The Three-dimensional Crystal Structure of the Catalytic Core of Cellobiohydrolase I from Trichoderma reesei
Authors: Divne, C. / Stahlberg, J. / Reinikainen, T. / Ruohonen, L. / Pettersson, G. / Knowles, J.K. / Teeri, T.T. / Jones, T.A.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Activity Studies and Crystal Structures of Catalytically Deficient Mutants of Cellobiohydrolase I from Trichoderma reesei
Authors: Stahlberg, J. / Divne, C. / Koivula, A. / Piens, K. / Claeyssens, M. / Teeri, T.T. / Jones, T.A.
#3: Journal: J.Mol.Biol. / Year: 1998
Title: High-resolution Crystal Structures Reveal how a Cellulose Chain is Bound in the 50a Long Tunnel of Cellobiohydrolase i from Trichoderma reesei
Authors: Divne, C. / Stahlberg, J. / Teeri, T.T. / Jones, T.A.
History
DepositionFeb 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Nov 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE CEL7A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3314
Polymers45,9921
Non-polymers3393
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.110, 83.340, 110.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-470-

CO

21A-740-

HOH

31A-866-

HOH

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Components

#1: Protein 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE CEL7A / CBH1 / CELLOBIOHYDROLASE I / EXOGLUCANASE / EXOCELLULASE


Mass: 45991.680 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1 - 434 / Mutation: E223S, A224H, L225V, T226A, D262G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus) / Plasmid: PEM-F5 / Production host: Hypocrea jecorina (fungus)
References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium acetate, PEG 5000 monomethyl-ether, glycerol, sodium morpholine-ethane-sulphonic acid, cobalt chloride , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mg/mlprotein1drop
210 mMsodium acetate1drop
318.75 %PEG5000 MME1reservoir
412.5 %glycerol1reservoir
520 mMsodium MES1reservoir
620 mM1reservoirCoCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.905
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 50885 / Num. obs: 50885 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 24.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.237 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 50924 / % possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 5.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1037 -RANDOM
Rwork0.24 ---
all0.24 50885 --
obs0.24 50885 100 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 16 354 3589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.24 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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