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- PDB-1h46: The catalytic module of Cel7D from Phanerochaete chrysosporium as... -

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Basic information

Entry
Database: PDB / ID: 1h46
TitleThe catalytic module of Cel7D from Phanerochaete chrysosporium as a chiral selector: Structural studies of its complex with the b-blocker (R)-propranolol
ComponentsEXOGLUCANASE I
KeywordsHYDROLASE / CELLULASE / CELLOBIOHYDROLASE / GLYCOSIDE HYDROLASE / ADRENERGIC BETA-BLOCKER / ENANTIOSELECTIVITY / ENANTIOMER SEPARATION
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / 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-RNP / Glucanase / Glucanase
Similarity search - Component
Biological speciesPHANEROCHAETE CHRYSOSPORIUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsMunoz, I.G. / Mowbray, S.L. / Stahlberg, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: The Catalytic Module of Cel7D from Phanerochaete Chrysosporium as a Chiral Selector: Structural Studies of its Complex with the Beta Blocker (R)-Propranolol
Authors: Munoz, I.G. / Mowbray, S.L. / Stahlberg, J.
History
DepositionOct 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Data collection / Other / Polymer sequence / Category: chem_comp / entity_poly / pdbx_database_status
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
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 / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 13, 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: EXOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2563
Polymers45,7771
Non-polymers4792
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.143, 46.557, 98.827
Angle α, β, γ (deg.)90.00, 102.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein EXOGLUCANASE I / 1 / 4-BETA-CELLOBIOHYDROLASE / CELLULASE / EXOCELLOBIOHYDROLASE I / CBH58 / CBH1 / CBH I / CBH1.2 EXOCELLULASE


Mass: 45777.141 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 19-449 / Source method: isolated from a natural source
Details: EXTRACELLULAR PROTEIN OBTAINED FROM THE FUNGUS PHANEROCHAETE CHRYSOSPORIUM
Source: (natural) PHANEROCHAETE CHRYSOSPORIUM (fungus) / Strain: K3
References: UniProt: Q09431, UniProt: Q7LHI2*PLUS, 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-RNP / (1E,2R)-1-(ISOPROPYLIMINO)-3-(1-NAPHTHYLOXY)PROPAN-2-OL


Mass: 257.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHYDROLYSES 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE AND CELLOTETRAOSE PRODUCING CELLOBIOSE. ...HYDROLYSES 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE AND CELLOTETRAOSE PRODUCING CELLOBIOSE. MEMBER OF THE CELLULASE FAMILY C THAT CONTAIN A FUNGAL-TYPE CELLULOSE-BINDING DOMAIN (CBD).
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: 2.6 Å3/Da / Density % sol: 42 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING-DROP VAPOUR DIFFUSION EXPERIMENTS INCLUDED 18 MG/ML PROTEIN, 100 MM TRIS-HCL, PH 7.0, 5 MM CACL2, 22.5% POLYETHYLENE GLYCOL 5000, 12% GLYCEROL AND 12.5% (R)-PROPRANOLOL.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 mg/mlprotein1drop
2100 mMTris-HCl1droppH7.0
35 mM1dropCa2Cl
422.5 %PEG50001drop
512 %glycerol1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 1.52→40 Å / Num. obs: 58656 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4.4 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 48.22 Å / % possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPI

1gpi


Resolution: 1.52→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.56 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2965 5.1 %RANDOM
Rwork0.169 ---
obs0.171 55639 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å2-0.83 Å2
2---0.41 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.52→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 33 325 3556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213307
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9464503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6553430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1615527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022545
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.31593
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.5462
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.329
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.690.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8581.52123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.78623403
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.65331184
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9654.51100
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 217
Rwork0.23 4055
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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