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- PDB-1eg1: ENDOGLUCANASE I FROM TRICHODERMA REESEI -

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Basic information

Entry
Database: PDB / ID: 1eg1
TitleENDOGLUCANASE I FROM TRICHODERMA REESEI
ComponentsENDOGLUCANASE I
KeywordsCELLULOSE DEGRADATION / ENDOGLUCANASE / MUTATION
Function / homology
Function and homology information


cellulose binding / 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 / 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
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsKleywegt, G.J. / Zou, J.-Y. / Jones, T.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 A resolution, and a comparison with related enzymes.
Authors: Kleywegt, G.J. / Zou, J.Y. / Divne, C. / Davies, G.J. / Sinning, I. / Stahlberg, J. / Reinikainen, T. / Srisodsuk, M. / Teeri, T.T. / Jones, T.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Studies on the Core Proteins of Cellobiohydrolase I and Endoglucanase I from Trichoderma Reesei
Authors: Divne, C. / Sinning, I. / Stahlberg, J. / Pettersson, G. / Bailey, M. / Siika-Aho, M. / Margolles-Clark, E. / Teeri, T. / Jones, T.A.
History
DepositionNov 26, 1996Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
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 / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Apr 3, 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
Revision 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE I
C: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2246
Polymers78,3392
Non-polymers8854
Water00
1
A: ENDOGLUCANASE I
C: ENDOGLUCANASE I
hetero molecules

A: ENDOGLUCANASE I
C: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,44812
Polymers156,6784
Non-polymers1,7708
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
Unit cell
Length a, b, c (Å)101.400, 101.400, 199.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.01124, 0.003167), (0.010845, -0.793189, 0.60888), (-0.004332, 0.608872, 0.793256)
Vector: 174.44016, -1.51428, 0.7017)

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Components

#1: Protein ENDOGLUCANASE I / EGI / ENDO-1 / 4-BETA-GLUCANASE I


Mass: 39169.566 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 1 - 371 / Mutation: DEL(372 - 436) / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / Plasmid: PEM-F5 / Variant: VTT-D-80133 / Strain: QM9414 / References: UniProt: P07981, 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.: 4
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63 %
Crystal growpH: 4.5 / Details: DESCRIBED IN REFERENCE 1., pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop contains equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMglucose1drop
31 Mammonium sulfate1reservoir
4100 mMammonium citrate1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.6→71.1 Å / Num. obs: 11696 / % possible obs: 92.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.117
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.404 / % possible all: 93.3
Reflection
*PLUS
Num. measured all: 45852
Reflection shell
*PLUS
% possible obs: 93.3 % / Num. unique obs: 3353

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
AMoREphasing
X-PLOR4refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMICOLA INSOLENS EG1

Resolution: 3.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: GROUPED TEMPERATURE-FACTORS WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 -8 %THIN RESOLUTION SHELLS
Rwork0.201 ---
obs0.201 10600 --
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 3.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 56 0 5528
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
Software
*PLUS
Name: X-PLOR / Version: 4 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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