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- PDB-2ovw: ENDOGLUCANASE I COMPLEXED WITH CELLOBIOSE -

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Basic information

Entry
Database: PDB / ID: 2ovw
TitleENDOGLUCANASE I COMPLEXED WITH CELLOBIOSE
ComponentsENDOGLUCANASE ICellulase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / ENDOGLUCANASE I / COMPLEXED WITH 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
beta-cellobiose / Endoglucanase type C
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSulzenbacher, G. / Davies, 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
DepositionApr 4, 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: 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _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

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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)181,88016
Polymers178,7414
Non-polymers3,13912
Water19,8351101
1
A: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4704
Polymers44,6851
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4704
Polymers44,6851
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4704
Polymers44,6851
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4704
Polymers44,6851
Non-polymers7853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.930, 78.310, 142.470
Angle α, β, γ (deg.)90.00, 96.98, 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.

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Components

#1: Protein
ENDOGLUCANASE I / Cellulase


Mass: 44685.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P46237, cellulase
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}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 / N-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 1101 / 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. 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.
Nonpolymer detailsA LIGAND CELLOBIOSE IS BOUND IN THE ACTIVE SITE OF EACH MOLECULE AND HAS THE RESIDUE NAME COB AND ...A LIGAND CELLOBIOSE IS BOUND IN THE ACTIVE SITE OF EACH MOLECULE AND HAS THE RESIDUE NAME COB 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: 2.09 Å3/Da / Density % sol: 40.6 %
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 VAPOR DIFFUSION THE NATIVE CRYSTALS WERE SOAKED FOR 1 HOUR IN STABILIZING SOLUTION CONTAINING 20 MM OF ...Details: 22 % PEG 8K, 0.2 M MAGNESIUM CHLORIDE, PH 6.5 FOR 0.1 M MOPS. METHOD: HANGING DROP VAPOR DIFFUSION THE NATIVE CRYSTALS WERE SOAKED FOR 1 HOUR IN STABILIZING SOLUTION CONTAINING 20 MM OF CELLOBIOSE., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / pH: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120-26 %(w/v)PEG80001reservoir
20.15-0.3 M1reservoirMgCl2
30.1 MMOPS1reservoirpH6.4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 23, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 57194 / % possible obs: 86.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.27 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.37 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.29 / % possible all: 59.9
Reflection shell
*PLUS
% possible obs: 54 %

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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: 2.3→15 Å / Cross valid method: FREE R / Details: X-PLOR 3.1 (BRUNGER) ALSO WAS USED.
RfactorNum. reflection% reflectionSelection details
Rwork0.209 ---
Rfree-2887 5 %RANDOM
obs-54116 86.4 %-
Displacement parametersBiso mean: 29.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12088 0 204 1101 13393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8412
X-RAY DIFFRACTIONp_mcangle_it2.8284
X-RAY DIFFRACTIONp_scbond_it4.3934
X-RAY DIFFRACTIONp_scangle_it5.6855
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1960.3
X-RAY DIFFRACTIONp_planar_tor2.37
X-RAY DIFFRACTIONp_staggered_tor20.820
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.925
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.209 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS

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