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- PDB-1dy4: CBH1 IN COMPLEX WITH S-PROPRANOLOL -

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Basic information

Entry
Database: PDB / ID: 1dy4
TitleCBH1 IN COMPLEX WITH S-PROPRANOLOL
ComponentsEXOGLUCANASE 1
KeywordsHYDROLASE / HYDROLASE(O-GLYCOSYL) / CELLULOSE DEAGRADATION / CHIRAL SEPARATION / GLYCOSIDASE / GLYCOPROTEIN
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
: / 1-(ISOPROPYLAMINO)-3-(1-NAPHTHYLOXY)-2-PROPANOL / Exoglucanase 1
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStahlberg, J. / Henriksson, H. / Divne, C. / Isaksson, R. / Pettersson, G. / Johansson, G. / Jones, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Structural Basis for Enantiomer Binding and Separation of a Common Beta-Blocker: Crystal Structure of Cellobiohydrolase Cel7A with Bound (S)-Propranolol at 1.9 A Resolution
Authors: Stahlberg, J. / Henriksson, H. / Divne, C. / Isaksson, R. / Pettersson, G. / Johansson, G. / Jones, T.A.
#1: 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.
#2: 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.
History
DepositionJan 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2011Group: Other
Revision 1.2Feb 12, 2014Group: Source and taxonomy
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jan 31, 2018Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.6Nov 20, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
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_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 2.2Dec 6, 2023Group: 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
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS IS REPRESENTED BY ... SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXOGLUCANASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8306
Polymers46,0111
Non-polymers8205
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.960, 83.110, 110.680
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

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Components

#1: Protein EXOGLUCANASE 1 / CELLOBIOHYDROLASE I / CEL7A / EXOCELLULASE / 1 / 4-BETA-CELLOBIOHYDROLASE / EXOCELLOBIOHYDROLASE I ...CELLOBIOHYDROLASE I / CEL7A / EXOCELLULASE / 1 / 4-BETA-CELLOBIOHYDROLASE / EXOCELLOBIOHYDROLASE I / CBHI / EXOGLUCANASE I


Mass: 46010.703 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 18-451 / Source method: isolated from a natural source / Source: (natural) TRICHODERMA REESEI (fungus) / Strain: QM9414
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.: 2
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-SNP / 1-(ISOPROPYLAMINO)-3-(1-NAPHTHYLOXY)-2-PROPANOL / S-PROPRANOLOL


Mass: 259.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21NO2
#4: Chemical ChemComp-CO / COBALT (II) ION


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


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE I222 CRYSTAL FORM DESCRIBED HERE REPRESENTS THE HIGHER SYMMETRY EQUIVALENT TO THE PSEUDO-I222 ...THE I222 CRYSTAL FORM DESCRIBED HERE REPRESENTS THE HIGHER SYMMETRY EQUIVALENT TO THE PSEUDO-I222 PRIMITIVE ORTHORHOMBIC CELL DESCRIBED PREVIOUSLY IN ENTRY 1CEL. THE COORDINATES GIVEN DEFINE THE STRUCTURE OF ONLY THE CATALYTIC DOMAIN (RESIDUES 1 - 434) OF THE 497 RESIDUES IN THE MATURE PROTEIN. THE N-TERMINUS IS PROTECTED BY A PYROGLUTAMATE RESIDUE.
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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROPS. EQUAL VOLUMES OF 9 MG/ML PROTEIN/7.5 MM S-PROPRANOLOL AND RESERVOIR SOLUTION CONTAINING 0.1 M MES (PH 7.0), 24% (W/V) MONOMETHYL ETHER PEG 5000, 15% GLYCEROL AND 10 MM COCL2.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
27.5 mM(S)-propanolol1drop
3100 mMMES1reservoir
424 %(w/v)mPEG50001reservoir
515 %(v/v)glycerol1reservoir
610 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: R-AXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→33.6 Å / Num. obs: 30518 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 32.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 12.3 / % possible all: 100
Reflection
*PLUS
Num. measured all: 375375
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CEL

5cel


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.22 2000 -
Rwork0.191 --
obs0.191 30516 100 %
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 49 342 3611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 28512 / Rfactor obs: 0.197 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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