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- PDB-1cec: A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO DISTINCT FAM... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1cec
TitleA COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO DISTINCT FAMILIES OF BETA-GLYCANASES
ComponentsENDOGLUCANASE CELC
KeywordsHYDROLASE (GLYCOSYL) / GLYCOSYL HYDROLASE / CELLULASE / FAMILY A/5 OF CELLULASES/GLYCOSYL HYDROLASES / CLOSTRIDIUM THERMOCELLUM / ENDOGLUCANASE C
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: 2.15 Å
AuthorsAlzari, P.M. / Dominguez, R.
Citation
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.
#1: Journal: Proteins / Year: 1994
Title: Characterization of Two Crystal Forms of Clostridium Thermocellum Endoglucanase Celc
Authors: Dominguez, R. / Souchon, H. / Alzari, P.M.
History
DepositionJun 7, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE CELC


Theoretical massNumber of molelcules
Total (without water)40,9481
Polymers40,9481
Non-polymers00
Water2,972165
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 = 1.73 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein ENDOGLUCANASE CELC / EGC / CELLULASE CELC / ENDO-1\ / 4-BETA-GLUCANASE CELC


Mass: 40948.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CELLULASE FAMILY A/5 / Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: NCIB 10682 / Gene: MC1061 / Plasmid: PCT301 / Gene (production host): MC1061 / 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.: 165 / 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
Temperature: 24 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMTris-HCl1drop
320 %PEG20001reservoir
40.2 Mcalcium acetate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 19891 / % possible obs: 90.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 20 Å / 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: 2.15→6 Å / σ(F): 3
RfactorNum. reflection
Rfree0.215 -
Rwork0.168 -
obs0.168 18363
Displacement parametersBiso mean: 31.51 Å2
Refinement stepCycle: LAST / Resolution: 2.15→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2778 0 0 165 2943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.62
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
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_deg23.62
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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