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- PDB-4eng: STRUCTURE OF ENDOGLUCANASE V CELLOHEXAOSE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 4eng
TitleSTRUCTURE OF ENDOGLUCANASE V CELLOHEXAOSE COMPLEX
ComponentsENDOGLUCANASE V CELLOHEXAOSE 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
alpha-cellotriose / 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: Non-polymer description / Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE V CELLOHEXAOSE COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5543
Polymers22,5451
Non-polymers1,0092
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.930, 51.980, 42.010
Angle α, β, γ (deg.)90.00, 97.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE V CELLOHEXAOSE COMPLEX


Mass: 22544.984 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE, RESIDUES 1 - 210 / Mutation: D10N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus) / References: UniProt: P43316, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS IS AN INACTIVE MUTANT (D10N) COMPLEX WITH THE SUBSTRATE CELLOHEXAOSE. TWO HALF CELLOHEXAOSES ...THIS IS AN INACTIVE MUTANT (D10N) COMPLEX WITH THE SUBSTRATE CELLOHEXAOSE. TWO HALF CELLOHEXAOSES ARE PRESENT IN THE ENZYME'S -4, -3, -2 AND +1, +2 AND +3 SUBSITES. ENDOGLUCANASE V IS FROM GLYCOSYL HYDROLASE FAMILY 45.
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: 2.01 Å3/Da / Density % sol: 38.83 %
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 CELLOHEXAOSE
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: 13502 / % possible obs: 95.1 % / Observed criterion σ(I): -999 / Redundancy: 3.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.56
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.48 / % possible all: 64

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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 /
RfactorNum. reflection
Rwork0.157 -
obs-13406
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 68 132 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0280.051
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.053
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.683
X-RAY DIFFRACTIONp_mcangle_it2.2615
X-RAY DIFFRACTIONp_scbond_it3.1844
X-RAY DIFFRACTIONp_scangle_it4.5066
X-RAY DIFFRACTIONp_plane_restr0.0070.016
X-RAY DIFFRACTIONp_chiral_restr0.110.15
X-RAY DIFFRACTIONp_singtor_nbd0.1640.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor17.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.920
X-RAY DIFFRACTIONp_special_tor

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