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- PDB-3ovw: ENDOGLUCANASE I NATIVE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 3ovw
TitleENDOGLUCANASE I NATIVE STRUCTURE
ComponentsENDOGLUCANASE I
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / ENDOGLUCANASE I / 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
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: 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 25, 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 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2556
Polymers89,3712
Non-polymers8854
Water7,602422
1
A: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1283
Polymers44,6851
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1283
Polymers44,6851
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.420, 81.940, 90.990
Angle α, β, γ (deg.)90.00, 105.97, 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.: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS STRUCTURE BELONGS TO FAMILY 7 OF GLYCOSYL HYDROLASES. THIS IS THE NATIVE ENZYME STRUCTURE. THE ...THIS STRUCTURE BELONGS TO FAMILY 7 OF GLYCOSYL HYDROLASES. THIS IS THE NATIVE ENZYME STRUCTURE. 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

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG 8K, 0.2 M MAGNESIUM CHLORIDE, PH 6.5 FOR 0.1 M MOPS. METHOD: HANGING DROP VAPOR DIFFUSION, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.2 M1reservoirMgCl2
20.1 MMOPS1reservoirpH6.5
310-20 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorDate: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 32773 / % possible obs: 91 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.185 / % possible all: 51.9
Reflection shell
*PLUS
% possible obs: 51 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE OF HUMICOLA INSOLENS EG I

Resolution: 2.3→18 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.225 --
Rwork0.158 --
obs-32757 91 %
Refinement stepCycle: LAST / Resolution: 2.3→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6070 0 56 422 6548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.1522
X-RAY DIFFRACTIONp_mcangle_it4.033
X-RAY DIFFRACTIONp_scbond_it4.9212
X-RAY DIFFRACTIONp_scangle_it6.4643
X-RAY DIFFRACTIONp_plane_restr0.0230.02
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2530.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1770.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor19.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 32757 / Rfactor all: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS

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