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- PDB-6grn: CELLOBIOHYDROLASE I (CEL7A) FROM Trichoderma reesei with S-dihydr... -

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Basic information

Entry
Database: PDB / ID: 6grn
TitleCELLOBIOHYDROLASE I (CEL7A) FROM Trichoderma reesei with S-dihydroxypropranolol in the active site
ComponentsExoglucanase 1Cellulose 1,4-beta-cellobiosidase
KeywordsHYDROLASE / CELLULASE / Glyco_hydro_7 / cellobiohydrolase / chiral selector
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
: / Chem-F9B / Exoglucanase 1
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSandgren, M. / Fagerstrom, A. / Widmalm, G. / Stahlberg, J.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Chemistry / Year: 2018
Title: Enantioselective Binding of Propranolol and Analogues Thereof to Cellobiohydrolase Cel7A.
Authors: Hamark, C. / Pendrill, R. / Landstrom, J. / Dotson Fagerstrom, A. / Sandgren, M. / Stahlberg, J. / Widmalm, G.
History
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.0Mar 11, 2020Group: Data collection / Polymer sequence / Category: chem_comp / entity_poly
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can
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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.value / _struct_conn.conn_type_id / _struct_conn.id / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6415
Polymers46,0111
Non-polymers6304
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-11 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.109, 83.318, 110.962
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-502-

CO

21A-1070-

HOH

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Components

#1: Protein Exoglucanase 1 / Cellulose 1,4-beta-cellobiosidase / 1 / 4-beta-cellobiohydrolase / Cellobiohydrolase 7A / Cel7A / Exocellobiohydrolase I / CBHI / Exoglucanase I


Mass: 46010.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Catalytic domain residues 1-434 / Source: (natural) Trichoderma reesei (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: Chemical ChemComp-F9B / 2-[[(2~{S})-3-naphthalen-1-yloxy-2-oxidanyl-propyl]amino]propane-1,3-diol


Mass: 291.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18% mPEG 5000, 10 mM sodium acetate (ph 5.0), 14% glycerol, 11 mM cobalt chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.115 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 1.78→40.4 Å / Num. obs: 34736 / % possible obs: 94.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Net I/σ(I): 8.7
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 4.85 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4455 / Rrim(I) all: 0.14 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EGN

1egn


Resolution: 1.79→35.31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.133 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18795 1748 5 %RANDOM
Rwork0.14531 ---
obs0.14745 32985 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.79→35.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 37 470 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023393
X-RAY DIFFRACTIONr_bond_other_d0.0020.022889
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9374645
X-RAY DIFFRACTIONr_angle_other_deg0.9636713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86325.772149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26615489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.948157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02782
X-RAY DIFFRACTIONr_nbd_refined0.2310.22316
X-RAY DIFFRACTIONr_nbd_other0.130.237
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7511.2091766
X-RAY DIFFRACTIONr_mcbond_other0.7421.2071765
X-RAY DIFFRACTIONr_mcangle_it1.2381.812216
X-RAY DIFFRACTIONr_mcangle_other1.2411.8112217
X-RAY DIFFRACTIONr_scbond_it1.0241.2771627
X-RAY DIFFRACTIONr_scbond_other1.0241.2771628
X-RAY DIFFRACTIONr_scangle_it1.6011.8852426
X-RAY DIFFRACTIONr_scangle_other1.6011.8852427
X-RAY DIFFRACTIONr_long_range_B_refined4.06410.8654301
X-RAY DIFFRACTIONr_long_range_B_other3.48210.2024048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 121 -
Rwork0.183 2338 -
obs--91.82 %

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