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- PDB-2eng: ENDOGLUCANASE V -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2eng
TitleENDOGLUCANASE V
ComponentsENDOGLUCANASE V
KeywordsHYDROLASE (ENDOGLUCANASE) / CELLULOSE DEGRADATION / GLYCOSIDASE
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
Biological speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsDavies, G.J. / Schulein, M.
Citation
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.
History
DepositionJun 29, 1995Processing site: BNL
SupersessionDec 7, 1996ID: 1ENG
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 V


Theoretical massNumber of molelcules
Total (without water)22,5461
Polymers22,5461
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.110, 51.680, 45.060
Angle α, β, γ (deg.)90.00, 109.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOGLUCANASE V


Mass: 22545.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Humicola insolens (fungus) / References: UniProt: P43316, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDOGLUCANASE V IS IN GLYCOSYL HYDROLASE FAMILY 45.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme1drop
220 mMTris-HCl1reservoirpH8.0
310-22 %(w/v)PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.48 Å

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Processing

SoftwareName: SHELXL / Classification: refinement
RefinementResolution: 1.5→10 Å
Details: THE SECOND (LESSER) CONFORMATION FOR THE SIDE CHAIN OF ASP 121 MAKES A STERIC CLASH WITH THE SIDE CHAIN OF HIS 119. HIS 119 HAS THEREFORE BEEN REFINED WITH A PARTIAL OCCUPANCY OF 0.6. THE ...Details: THE SECOND (LESSER) CONFORMATION FOR THE SIDE CHAIN OF ASP 121 MAKES A STERIC CLASH WITH THE SIDE CHAIN OF HIS 119. HIS 119 HAS THEREFORE BEEN REFINED WITH A PARTIAL OCCUPANCY OF 0.6. THE ISOTROPIC TEMPERATURE FACTORS GIVEN ARE CALCULATED BY CONVERSION FROM THE ANISOTROPIC DISPLACEMENT PARAMETERS. A COORDINATE SET WITH ANISOTROPIC DISPLACEMENT PARAMETERS WILL BE SUBMITTED SOON.
RfactorNum. reflection% reflection
Rfree0.154 --
obs0.105 -97 %
all-28814 -
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 0 244 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONs_bond_d0.0120.03
X-RAY DIFFRACTIONs_angle_d0.0310.05
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELX / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.105
Solvent computation
*PLUS
Displacement parameters
*PLUS

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