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- PDB-4ovw: ENDOGLUCANASE I COMPLEXED WITH EPOXYBUTYL CELLOBIOSE -

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Basic information

Entry
Database: PDB / ID: 4ovw
TitleENDOGLUCANASE I COMPLEXED WITH EPOXYBUTYL CELLOBIOSE
ComponentsENDOGLUCANASE I
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / ENDOGLUCANASE I / COMPLEX WITH EPOXYBUTYL CELLOBIOSE / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
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
Chem-IN1 / Endoglucanase type C
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDavies, G.J. / Schulein, M.
Citation
Journal: Biochemistry / Year: 1997
Title: Structure of the endoglucanase I from Fusarium oxysporum: native, cellobiose, and 3,4-epoxybutyl beta-D-cellobioside-inhibited forms, at 2.3 A resolution.
Authors: Sulzenbacher, G. / Schulein, M. / Davies, G.J.
#1: Journal: Biochemistry / Year: 1996
Title: Structure of the Fusarium Oxysporum Endoglucanase I with a Nonhydrolyzable Substrate Analogue: Substrate Distortion Gives Rise to the Preferred Axial Orientation for the Leaving Group
Authors: Sulzenbacher, G. / Driguez, H. / Henrissat, B. / Schulein, M. / Davies, G.J.
#2: Journal: Gene / Year: 1994
Title: The Use of Conserved Cellulase Family-Specific Sequences to Clone Cellulase Homologue Cdnas from Fusarium Oxysporum
Authors: Sheppard, P.O. / Grant, F.J. / Oort, P.J. / Sprecher, C.A. / Foster, D.C. / Hagen, F.S. / Upshall, A. / Mcknight, G.L. / O'Hara, P.J.
History
DepositionOct 6, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 3.1Apr 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 3.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,4946
Polymers89,3712
Non-polymers1,1234
Water12,592699
1
A: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2473
Polymers44,6851
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2473
Polymers44,6851
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.940, 82.620, 73.160
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE I


Mass: 44685.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P46237, 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: Sugar ChemComp-IN1 / 4-(beta-D-glucopyranosyloxy)-2,2-dihydroxybutyl propanoate / PROPIONIC ACID 2,2-DIHYDROXY-3-(1-GLUCOPYRANOSYLOXY)-METHYLPROPYL ESTER / 4-(beta-D-glucosyloxy)-2,2-dihydroxybutyl propanoate / 4-(D-glucosyloxy)-2,2-dihydroxybutyl propanoate / 4-(glucosyloxy)-2,2-dihydroxybutyl propanoate


Type: D-saccharide / Mass: 340.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H24O10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE C-TERMINAL RESIDUES ARE EITHER DISORDERED OR ABSENT (C-TERMINAL DEGRADATION). MASS SPECTROMETRY ...THE C-TERMINAL RESIDUES ARE EITHER DISORDERED OR ABSENT (C-TERMINAL DEGRADATION). MASS SPECTROMETRY ANALYSIS SHOWS THAT A MIXTURE OF VARIOUS C-TERMINAL DEGRADATIONS IS PRESENT.
Has protein modificationY
Nonpolymer detailsTHE CATALYTIC NUCLEOPHILE GLU 197 IS COVALENTLY LABELLED WITH THE EPOXIDE REAGENT. FOR EASE OF ...THE CATALYTIC NUCLEOPHILE GLU 197 IS COVALENTLY LABELLED WITH THE EPOXIDE REAGENT. FOR EASE OF REFINEMENT SOME OF THE ATOMS OF GLU 197 ARE NOW TREATED AS LIGAND ATOMS IN THE "INH" MOIETY. THIS LIGAND BINDS AS BOTH R AND S STEREOISOMERS WHICH HAVE BEEN MODELLED WITH OCCUPANCIES OF 0.7 AND 0.3, RESPECTIVELY.

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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: 2.29 Å3/Da / Density % sol: 46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 22 % MEPEG 2K, 0.2 M MAGNESIUM CHLORIDE, PH 7.5 FOR 0.1 M TRIS. METHOD: HANGING DROP VAPOR DIFFUSION. THE PROTEIN SAMPLE HAD PREVIOUSLY BEEN INHIBITED WITH 8.25 MMOL 3,4-EPOXYBUTYL B-D- ...Details: 22 % MEPEG 2K, 0.2 M MAGNESIUM CHLORIDE, PH 7.5 FOR 0.1 M TRIS. METHOD: HANGING DROP VAPOR DIFFUSION. THE PROTEIN SAMPLE HAD PREVIOUSLY BEEN INHIBITED WITH 8.25 MMOL 3,4-EPOXYBUTYL B-D-CELLOBIOSIDE FOR 3HRS., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / pH: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH7.7
216-22 %mPEG20001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→18 Å / % possible obs: 88 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.201 / % possible all: 47
Reflection shell
*PLUS
% possible obs: 47 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE (2 MOLECULES IN ASYMMETRIC UNIT)

Highest resolution: 2.3 Å / Cross valid method: FREE R / Details: X-PLOR 3.1 (BRUNGER) ALSO WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1587 5 %RANDOM
Rwork0.18 ---
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 74 699 6833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0420.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8872
X-RAY DIFFRACTIONp_mcangle_it2.6894
X-RAY DIFFRACTIONp_scbond_it2.6034
X-RAY DIFFRACTIONp_scangle_it3.6565
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1460.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2580.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.210.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor20.320
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.225
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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