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- PDB-1q2b: CELLOBIOHYDROLASE CEL7A WITH DISULPHIDE BRIDGE ADDED ACROSS EXO-L... -

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Basic information

Entry
Database: PDB / ID: 1q2b
TitleCELLOBIOHYDROLASE CEL7A WITH DISULPHIDE BRIDGE ADDED ACROSS EXO-LOOP BY MUTATIONS D241C AND D249C
ComponentsEXOCELLOBIOHYDROLASE I
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / GLYCOSIDASE / GLYCOPROTEIN / GLYCOSYLATED PROTEIN / DISULPHIDE 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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsStahlberg, J. / Harris, M. / Jones, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Engineering the exo-loop of Trichoderma reesei cellobiohydrolase, Cel7A. A comparison with Phanerochaete chrysosporium Cel7D.
Authors: von Ossowski, I. / Stahlberg, J. / Koivula, A. / Piens, K. / Becker, D. / Boer, H. / Harle, R. / Harris, M. / Divne, C. / Mahdi, S. / Zhao, Y. / Driguez, H. / Claeyssens, M. / Sinnott, M.L. / Teeri, T.T.
#1: 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.
#2: 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
DepositionJul 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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 2.2Oct 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 2.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXOCELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3844
Polymers46,0451
Non-polymers3393
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.170, 83.140, 110.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1307-

HOH

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Components

#1: Protein EXOCELLOBIOHYDROLASE I / E.C.3.2.1.91 / EXOGLUCANASE I / CBHI / 1 / 4-beta-cellobiohydrolase / cellulose 1 / 4-beta-cellobiosidase


Mass: 46044.848 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN 1-434 / Mutation: D241C, D249C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus) / Strain: QM9414 / Gene: cbh1 / Variant: VTT-D-93201 / Plasmid: PEM-F5 / Production host: Hypocrea jecorina (fungus) / Strain (production host): VTT-D-93201
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


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


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 5000 monomethyl ether, sodium morpholine-ethane-sulphonic acid, glycerol, cobalt chloride, sodium acetate, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11-5 mg/mlprotein1drop
210 mMsodium acetate1droppH5.0
318-22 %(w/v)mPEG50001reservoir
40.1 Msodium morpholine ethane sulphonic acid1reservoirpH6.0
510 mM1reservoirCoCl2
612.5 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.986 / Wavelength: 0.986 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 23, 1998 / Details: mirror
RadiationMonochromator: Single asymmetrically cut Si(111) crystal with horizontal diffraction plane
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.986 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 46521 / Num. obs: 46521 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 4.11 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 0.38 % / Rmerge(I) obs: 0.147 / % possible all: 95.8
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 40 Å / Redundancy: 4 %
Reflection shell
*PLUS
% possible obs: 95.8 % / Redundancy: 3.8 %

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→40 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.223 893 1.9 %RANDOM
Rwork0.207 ---
all-46518 --
obs-46518 92 %-
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 16 357 3593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 45625 / % reflection Rfree: 2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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