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- PDB-2exo: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE BETA-1,4-GLYCANA... -

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Basic information

Entry
Database: PDB / ID: 2exo
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE BETA-1,4-GLYCANASE CEX FROM CELLULOMONAS FIMI
ComponentsEXO-1,4-BETA-D-GLYCANASE
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Exoglucanase/xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWhite, A. / Withers, S.G. / Gilkes, N.R. / Rose, D.R.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of the catalytic domain of the beta-1,4-glycanase cex from Cellulomonas fimi.
Authors: White, A. / Withers, S.G. / Gilkes, N.R. / Rose, D.R.
History
DepositionJul 11, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXO-1,4-BETA-D-GLYCANASE


Theoretical massNumber of molelcules
Total (without water)34,0521
Polymers34,0521
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.147, 88.147, 81.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS CONFORMATION - THR 81 / 2: CIS PROLINE - PRO 241

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Components

#1: Protein EXO-1,4-BETA-D-GLYCANASE


Mass: 34051.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria)
References: UniProt: P07986, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop / Details: Bedarkar, S., (1992) J.Mol. Biol, 228, 693.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
165 mg/mlCex1dropin water
27.5-10 %PEG40001drop
30.1 Msodium acetate1drop
47.5-10 %PEG40001reservoir
50.1 Msodium acetate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 29059 / % possible obs: 94 % / Num. measured all: 128888 / Rmerge(I) obs: 0.061

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.266 -
Rwork0.213 -
obs0.213 24763
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 0 65 2465
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.217 / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.86
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.63

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