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- PDB-1cem: ENDOGLUCANASE A (CELA) CATALYTIC CORE, RESIDUES 33-395 -

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Basic information

Entry
Database: PDB / ID: 1cem
TitleENDOGLUCANASE A (CELA) CATALYTIC CORE, RESIDUES 33-395
ComponentsCELLULASE CELA (1,4-BETA-D-GLUCAN-GLUCANOHYDROLASE)
KeywordsGLYCOSYLTRANSFERASE / GLYCOSYL HYDROLASE / CELLULASE / FAMILY D/8 OF GLYCOSYL HYDROLASES / CLOSTRIDIUM THERMOCELLUM
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily ...Glycoside hydrolase, family 8, conserved site / Glycosyl hydrolases family 8 signature. / Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Alpha
Similarity search - Domain/homology
Endoglucanase A / Endoglucanase A
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsAlzari, P.M.
Citation
Journal: Structure / Year: 1996
Title: The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum.
Authors: Alzari, P.M. / Souchon, H. / Dominguez, R.
#1: Journal: Proteins / Year: 1996
Title: Crystallization of a Family 8 Cellulase from Clostridium Thermocellum
Authors: Souchon, H. / Beguin, P. / Alzari, P.M.
History
DepositionDec 4, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_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: CELLULASE CELA (1,4-BETA-D-GLUCAN-GLUCANOHYDROLASE)


Theoretical massNumber of molelcules
Total (without water)40,3451
Polymers40,3451
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.118, 63.518, 104.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CELLULASE CELA (1,4-BETA-D-GLUCAN-GLUCANOHYDROLASE) / ENDO-1 / 4-BETA-GLUCANASE A


Mass: 40345.277 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE RESIDUES 33-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: NCIB 10682 / Gene: CELA / Plasmid: PCT128 (PTZ18R) / Production host: Escherichia coli (E. coli)
References: UniProt: P04955, UniProt: A3DC29*PLUS, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE COORDINATES REPORTED IN THIS ENTRY ARE THOSE OF THE CATALYTIC CORE, RESIDUES 33 - 395, OBTAINED ...THE COORDINATES REPORTED IN THIS ENTRY ARE THOSE OF THE CATALYTIC CORE, RESIDUES 33 - 395, OBTAINED AFTER PAPAIN DIGESTION OF THE PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal
*PLUS
Density % sol: 38 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Details: macroseeding, Souchon, H., (1996) Proteins: Struct.,Funct., Genet., 25, 134.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MTris11pH7.5
20.2 M11NaCl
317 %PEG400011
40.1 MTris-HCl12pH7.2
515 %PEG800012

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 39653 / % possible obs: 96.9 % / Redundancy: 6.26 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Num. obs: 39868 / Num. measured all: 249508
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.155

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
RefinementResolution: 1.65→10 Å
RfactorNum. reflection
Rfree0.191 -
Rwork0.162 -
obs0.162 39653
Displacement parametersBiso mean: 14.26 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 0 266 3116
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_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38

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