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- PDB-1dym: Humicola insolens Endocellulase Cel7B (EG 1) E197A Mutant -

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Basic information

Entry
Database: PDB / ID: 1dym
TitleHumicola insolens Endocellulase Cel7B (EG 1) E197A Mutant
ComponentsENDOGLUCANASE I
KeywordsHYDROLASE / ENDOGLUCANASE / CELLULOSE DEGRADATION / GLYCOSIDASE / GLYCOPROTEIN / GLYCOSYNTHASE / GLYCOSIDE HYDROLASE FAMILY 7
Function / homology
Function and homology information


cellulase / cellulase activity / 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 / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDavies, G.J. / Moraz, O. / Driguez, H. / Schulein, M.
Citation
Journal: Biochem.J. / Year: 1998
Title: Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate.
Authors: MacKenzie, L.F. / Sulzenbacher, G. / Divne, C. / Jones, T.A. / Woldike, H.F. / Schulein, M. / Withers, S.G. / Davies, G.J.
#1: Journal: J.Biotechnol. / Year: 1997
Title: Oligosaccharide Specificity of a Family 7 Endoglucanase: Insertion of Potential Sugar-Binding Subsites
Authors: Davies, G.J. / Ducros, V. / Lewis, R.J. / Borchert, T.V. / Schulein, M.
History
DepositionFeb 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _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 / 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 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 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: PART OF THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. ORDER TO ... SHEET DETERMINATION METHOD: PART OF THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, AND 3 OF SHEETS A AND A1 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9953
Polymers44,5521
Non-polymers4422
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.969, 74.284, 60.146
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE I / CELLULASE / FAMILY 7 ENDOGLUCANASE / ENDO-1 / 4-BETA-GLUCANASE


Mass: 44552.109 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PYROGLUTAMATE POST-TRANSLATIONAL MODIFICATION AT RESIDUE 1, N-LINKED N-ACETYLGLUCOSAMINE ON RESIDUE ASNS 89 AND 247
Source: (gene. exp.) HUMICOLA INSOLENS (fungus) / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: P56680, cellulase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growpH: 8 / Details: 20-30% PEG 4K, 20 MM TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 43135 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 19.7
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.45 / % possible all: 100

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A39 NATIVE STRUCTURE

2a39


Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2171 5 %RANDOM
Rwork0.158 ---
obs-43029 100 %-
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 28 595 3706
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it33
X-RAY DIFFRACTIONp_mcangle_it3.65
X-RAY DIFFRACTIONp_scbond_it4.84
X-RAY DIFFRACTIONp_scangle_it5.86
X-RAY DIFFRACTIONp_plane_restr0.01320.02
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2490.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1140.3
X-RAY DIFFRACTIONp_planar_tor4.67
X-RAY DIFFRACTIONp_staggered_tor14.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.520
X-RAY DIFFRACTIONp_special_tor

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