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- PDB-3eng: STRUCTURE OF ENDOGLUCANASE V CELLOBIOSE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 3eng
TitleSTRUCTURE OF ENDOGLUCANASE V CELLOBIOSE COMPLEX
ComponentsENDOGLUCANASE V CELLOBIOSE COMPLEX
KeywordsGLYCOSYL HYDROLASE / HYDROLASE / ENDOGLUCANASE
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 45 / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-cellobiose / Endoglucanase-5
Similarity search - Component
Biological speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDavies, G.J. / Schulein, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure determination and refinement of the Humicola insolens endoglucanase V at 1.5 A resolution.
Authors: Davies, G.J. / Dodson, G. / Moore, M.H. / Tolley, S.P. / Dauter, Z. / Wilson, K.S. / Rasmussen, G. / Schulein, M.
#1: Journal: Biochemistry / Year: 1995
Title: Structures of Oligosaccharide-Bound Forms of the Endoglucanase V from Humicola Insolens at 1.9 A Resolution
Authors: Davies, G.J. / Tolley, S.P. / Henrissat, B. / Hjort, C. / Schulein, M.
#2: Journal: Nature / Year: 1993
Title: Structure and Function of Endoglucanase V
Authors: Davies, G.J. / Dodson, G.G. / Hubbard, R.E. / Tolley, S.P. / Dauter, Z. / Wilson, K.S. / Hjort, C. / Mikkelsen, J.M. / Rasmussen, G. / Schulein, M.
History
DepositionOct 17, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 2.0Jul 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 / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_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.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / 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

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Assembly

Deposited unit
A: ENDOGLUCANASE V CELLOBIOSE COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2272
Polymers22,8841
Non-polymers3421
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.750, 56.180, 37.370
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE V CELLOBIOSE COMPLEX


Mass: 22884.371 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE, RESIDUES 1 - 210 / Source method: isolated from a natural source / Source: (natural) Humicola insolens (fungus) / References: UniProt: P43316, 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.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDOGLUCANASE V IS FROM GLYCOSYL HYDROLASE FAMILY 45.

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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: 1.91 Å3/Da / Density % sol: 35.62 %
Crystal growpH: 8
Details: 10MG/ML ENZYME IN 20MM TRIS-HCL BUFFER PH 8.0. PRECIPITANT 18%(W/V) PEG 8K. CO-CRYSTALLISED WITH 5MM CELLOBIOSE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Davies, G.J., (1993) Nature, 365, 362.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 %PEG80001reservoir
212 mg/mlprotein1drop
310 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 13151 / % possible obs: 96.3 % / Observed criterion σ(I): -999 / Redundancy: 3.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 7.44 / % possible all: 78.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4(ROTAVATA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ENG

2eng


Resolution: 1.9→10 Å
Details: THIS IS A COMPLEX WITH THE PRODUCT CELLOBIOSE. THIS IS BOUND IN THE +1 AND +2 SUBSITES OF THE ENZYME. THESE ARE LABELLED AS THE E AND F RESIDUES OF CELLOBIOSE. IT WAS SOLVED BY MOLECULAR ...Details: THIS IS A COMPLEX WITH THE PRODUCT CELLOBIOSE. THIS IS BOUND IN THE +1 AND +2 SUBSITES OF THE ENZYME. THESE ARE LABELLED AS THE E AND F RESIDUES OF CELLOBIOSE. IT WAS SOLVED BY MOLECULAR REPLACEMENT USING THE NATIVE EGV STRUCTURE DESCRIBED IN REFERENCE 1 (ABOVE)
RfactorNum. reflection
Rwork0.145 -
obs-13070
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 23 152 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6213
X-RAY DIFFRACTIONp_mcangle_it2.1745
X-RAY DIFFRACTIONp_scbond_it2.9454
X-RAY DIFFRACTIONp_scangle_it4.4136
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1190.15
X-RAY DIFFRACTIONp_singtor_nbd0.1610.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor16.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.620
X-RAY DIFFRACTIONp_special_tor

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