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- PDB-1gpi: Cellobiohydrolase Cel7D (CBH 58) from Phanerochaete chrysosporium... -

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Basic information

Entry
Database: PDB / ID: 1gpi
TitleCellobiohydrolase Cel7D (CBH 58) from Phanerochaete chrysosporium. Catalytic module at 1.32 Angstrom resolution
ComponentsEXOGLUCANASE I
KeywordsHYDROLASE / GLYCOSIDASE / CELLULASE / BETA-GLUCANASE / GLYCOPROTEIN / CELLULOSE DEGRADATION / ENZYME / REACTION CENTER / EXTRACELLULAR / EXOGLUCANASE
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
Glucanase / Glucanase
Similarity search - Component
Biological speciesPHANEROCHAETE CHRYSOSPORIUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsMunoz, I.G. / Mowbray, S.L. / Stahlberg, J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Family 7 Cellobiohydrolases from Phanerochaete Chrysosporium: Crystal Structure of the Catalytic Module of Cel7D (Cbh58) at 1.32 Angstrom Resolution and Homology Models of the Isozymes.
Authors: Munoz, I.G. / Ubhayasekera, W. / Henriksson, H. / Szabo, I. / Pettersson, G. / Johansson, G. / Mowbray, S.L. / Stahlberg, J.
History
DepositionNov 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Mar 29, 2017Group: Structure summary
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_special_symmetry / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _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
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
A: EXOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9982
Polymers45,7771
Non-polymers2211
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.307, 46.625, 99.079
Angle α, β, γ (deg.)90.00, 103.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2364-

HOH

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Components

#1: Protein EXOGLUCANASE I / 1 / 4-BETA-D-GLUCAN CELLOBIOHYDROLASE CEL7D / EXOCELLOBIOHYDROLASE I / CELLOBIOHYDROLASE I / CBH58 ...1 / 4-BETA-D-GLUCAN CELLOBIOHYDROLASE CEL7D / EXOCELLOBIOHYDROLASE I / CELLOBIOHYDROLASE I / CBH58 / CBH1 / CBH I / CBH1.2


Mass: 45777.141 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 19-450 / Source method: isolated from a natural source
Details: EXTRACELLULAR PROTEIN OBTAINED FROM THE FED-BATCH CULTIVATION OF P. CHRYSOSPORIUM STRAIN K3 USING CELLULOSE (AVICEL) AS A CARBON SOURCE
Source: (natural) PHANEROCHAETE CHRYSOSPORIUM (fungus) / Strain: K3
References: UniProt: Q09431, UniProt: Q7LIJ0*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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREMOVES CELLOBIOSE (DISSACCHARIDE) FROM THE NON-REDUCING END OF THE CELLULOSE POLYMER CHAIN.

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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: 42 %
Crystal growpH: 7
Details: 22.5% PEG5000, 5 MM CACL2, 10 MM TRIS-HCL, PH 7.0, 12.5% GLYCEROL
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
212.5 mMR-propanolol1drop
31 mMsodium acetate1droppH5.0
427.5 %(w/v)PEG5000 MME1reservoir
52 mM1reservoirCaCl2
610 mMTris-HCl1reservoirpH7.0
710 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.906
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906 Å / Relative weight: 1
ReflectionResolution: 1.32→13 Å / Num. obs: 89559 / % possible obs: 98.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 17.2
Reflection shellResolution: 1.32→1.34 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4 / % possible all: 96.6
Reflection
*PLUS
Lowest resolution: 13 Å
Reflection shell
*PLUS
% possible obs: 96.6 % / Mean I/σ(I) obs: 4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CEL

2cel


Resolution: 1.32→13 Å / SU B: 3.058 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 8965 10.1 %RANDOM
Rwork0.213 ---
obs0.216 80227 98.96 %-
Refinement stepCycle: LAST / Resolution: 1.32→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 14 447 3659
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 13 Å / Rfactor obs: 0.1875 / Rfactor Rfree: 0.2269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2

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