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- PDB-1ovw: ENDOGLUCANASE I COMPLEXED WITH NON-HYDROLYSABLE SUBSTRATE ANALOGUE -

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Basic information

Entry
Database: PDB / ID: 1ovw
TitleENDOGLUCANASE I COMPLEXED WITH NON-HYDROLYSABLE SUBSTRATE ANALOGUE
ComponentsENDOGLUCANASE I
KeywordsHYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDASE / GLYCOPROTEIN
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
4-thio-beta-D-glucopyranosyl-(1->4)-4-thio-beta-D-glucopyranosyl-(1->4)-1,4-dithio-beta-D-glucopyranose / Endoglucanase type C
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSulzenbacher, G. / Davies, G.J. / Schulein, M.
Citation
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.
#1: 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.
#2: Journal: J.Carbohydr.Chem. / Year: 1993
Title: 4-Thiocellooligosaccharides: Their Synthesis and Use as Inhibitors of Cellulases Inhibitors of Cellulases
Authors: Schou, C. / Rasmussen, G. / Schulein, M. / Henrissat, B. / Driguez, H.
History
DepositionOct 17, 1996Processing site: BNL
Revision 1.0Oct 29, 1997Provider: 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: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / 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 / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_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 3.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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
C: ENDOGLUCANASE I
D: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,27516
Polymers173,2314
Non-polymers4,04412
Water19,3121072
1
B: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3194
Polymers43,3081
Non-polymers1,0113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3194
Polymers43,3081
Non-polymers1,0113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3194
Polymers43,3081
Non-polymers1,0113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3194
Polymers43,3081
Non-polymers1,0113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.155, 78.279, 142.461
Angle α, β, γ (deg.)90.00, 96.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE COORDINATES GIVEN DEFINE THE STRUCTURE OF ENDOGLUCANASE I AND COMPRISE RESIDUES 1 - 398 OF THE 412 RESIDUES IN THE MATURE PROTEIN. THERE ARE FOUR COPIES OF THE MOLECULE IN THE ASYMMETRIC UNIT WITH CHAIN IDENTIFIERS A, B, C AND D. THE SOLVENT STRUCTURE HAS CHAIN IDENTIFIERS A, B, C AND D.

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Components

#1: Protein
ENDOGLUCANASE I


Mass: 43307.711 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P46237, cellulase
#2: Polysaccharide
4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose / 4-thio-beta-D-glucopyranosyl-(1->4)-4-thio-beta-D-glucopyranosyl-(1->4)-1 / 4-dithio-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 568.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: 4-thio-beta-D-glucopyranosyl-(1->4)-4-thio-beta-D-glucopyranosyl-(1->4)-1,4-dithio-beta-D-glucopyranose
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5_1*S][a2122h-1b_1-5][a2122h-1b_1-5_4*S]/1-2-3/a4-b1*S*_b4-c1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1SH4SH]{[(4+S)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp4SH]{}}}LINUCSPDB-CARE
#3: 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.: 8
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1072 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDOGLUCANASE I BELONGS TO GLYCOSYL HYDROLASE FAMILY 7. THE ENZYME HAS 4 SUBSITES FOR SUGAR BINDING ...ENDOGLUCANASE I BELONGS TO GLYCOSYL HYDROLASE FAMILY 7. THE ENZYME HAS 4 SUBSITES FOR SUGAR BINDING AND PERFORMS CATALYSIS WITH RETENTION OF CONFIGURATION AT THE ANOMERIC CARBON.
Has protein modificationY
Nonpolymer detailsA LIGAND THIO-CELLOPENTAOSE IS BOUND IN THE ACTIVE SITE OF EACH MOLECULE AND HAS THE RESIDUE NAME ...A LIGAND THIO-CELLOPENTAOSE IS BOUND IN THE ACTIVE SITE OF EACH MOLECULE AND HAS THE RESIDUE NAME DP5 AND CHAIN IDENTIFIERS A, B, C AND D.

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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: 40.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 22 % PEG 8K, 0.2 M MAGNESIUM CHLORIDE, PH 6.5 FOR 0.1 M MOPS METHOD: HANGING DROP VAPOUR DIFFUSION THE NATIVE CRYSTALS WERE SOAKED FOR 1 HOUR IN STABILISING SOLUTION CONTAINING 5 MM OF THIO- ...Details: 22 % PEG 8K, 0.2 M MAGNESIUM CHLORIDE, PH 6.5 FOR 0.1 M MOPS METHOD: HANGING DROP VAPOUR DIFFUSION THE NATIVE CRYSTALS WERE SOAKED FOR 1 HOUR IN STABILISING SOLUTION CONTAINING 5 MM OF THIO-CELLOPENTAOSE, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlenzyme1drop
2100 mMMOPS1drop
322 %PEG80001reservoir
4200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 29, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 38998 / % possible obs: 94.7 % / Redundancy: 2.1 % / Biso Wilson estimate: 37.51 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 1.05 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.49 / % possible all: 94.96
Reflection
*PLUS
Num. measured all: 82217

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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)

Resolution: 2.7→15 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1952 5 %RANDOM
Rwork0.197 ---
obs-36855 89.49 %-
Displacement parametersBiso mean: 24.31 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12092 0 248 1072 13412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4512
X-RAY DIFFRACTIONp_mcangle_it2.2333
X-RAY DIFFRACTIONp_scbond_it2.9943
X-RAY DIFFRACTIONp_scangle_it4.1334
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0760.1
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2220.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor22.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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