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- PDB-1ceo: CELLULASE (CELC) MUTANT WITH GLU 140 REPLACED BY GLN -

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Basic information

Entry
Database: PDB / ID: 1ceo
TitleCELLULASE (CELC) MUTANT WITH GLU 140 REPLACED BY GLN
ComponentsCELLULASE CELC
KeywordsCELLULOSE DEGRADATION / GLYCOSYL HYDROLASE / CELLULASE / FAMILY A/5 OF GLYCOSYL HYDROLASES / CLOSTRIDIUM THERMOCELLUM
Function / homology
Function and homology information


cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endoglucanase C / Endoglucanase C
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsDominguez, R. / Alzari, P.M.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The crystal structure of a family 5 endoglucanase mutant in complexed and uncomplexed forms reveals an induced fit activation mechanism.
Authors: Dominguez, R. / Souchon, H. / Lascombe, M. / Alzari, P.M.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: A Common Protein Fold and Similar Active Site in Two Distinct Families of Beta-Glycanases
Authors: Dominguez, R. / Souchon, H. / Spinelli, S. / Dauter, Z. / Wilson, K.S. / Chauvaux, S. / Beguin, P. / Alzari, P.M.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1992
Title: Site-Directed Mutagenesis of Conserved Residues of Clostridium Thermocellum Endoglucanase Celc
Authors: Navas, J. / Beguin, P.
History
DepositionDec 4, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLULASE CELC


Theoretical massNumber of molelcules
Total (without water)40,9471
Polymers40,9471
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.400, 84.330, 87.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 202 / 2: CIS PROLINE - PRO 226
3: TRP 313 - ASN 314 OMEGA = 1.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein CELLULASE CELC / 1 / 4-BETA-D-GLUCAN-GLUCANOHYDROLASE / ENDO-1 / 4-BETA-GLUCANASE C


Mass: 40947.352 Da / Num. of mol.: 1 / Mutation: E140Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: NCIB 10682 / Plasmid: PCT306 (PUC9) / Production host: Escherichia coli (E. coli)
References: UniProt: P07985, UniProt: P0C2S3*PLUS, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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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: 46.87 %
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-ID
122-25 %PEG200011
20.1 MTris-HCl11
3mg/mlprotein11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 34277 / % possible obs: 97.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Num. measured all: 195009 / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.9→10 Å
RfactorNum. reflection
Rfree0.222 -
Rwork0.194 -
obs0.194 29900
Displacement parametersBiso mean: 25.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 0 288 3071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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