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- PDB-1edg: SINGLE CRYSTAL STRUCTURE DETERMINATION OF THE CATALYTIC DOMAIN OF... -

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Basic information

Entry
Database: PDB / ID: 1edg
TitleSINGLE CRYSTAL STRUCTURE DETERMINATION OF THE CATALYTIC DOMAIN OF CELCCA CARRIED OUT AT 15 DEGREE C
ComponentsENDOGLUCANASE A
KeywordsCELLULOSE DEGRADATION / FAMILY A / CELLULASES / XYLANASES / FAMILY 5 OF GLYCOSYL HYDROLASE
Function / homology
Function and homology information


cellulase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
: / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 ...: / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsDucros, V. / Czjzek, M. / Haser, R.
Citation
Journal: Structure / Year: 1995
Title: Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5.
Authors: Ducros, V. / Czjzek, M. / Belaich, A. / Gaudin, C. / Fierobe, H.P. / Belaich, J.P. / Davies, G.J. / Haser, R.
#1: Journal: J.Bacteriol. / Year: 1991
Title: Characterization of Endoglucanase a from Clostridium Cellulolyticum
Authors: Fierobe, H.P. / Gaudin, C. / Belaich, A. / Loutfi, M. / Faure, E. / Bagnara, C. / Baty, D. / Belaich, J.P.
History
DepositionJul 7, 1995Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE A


Theoretical massNumber of molelcules
Total (without water)43,1351
Polymers43,1351
Non-polymers00
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.400, 76.200, 113.500
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 ENDOGLUCANASE A / ENDO-(1 / 4)-BETA-GLUCANASE / CELCCA


Mass: 43135.414 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, C TERMINUS TRUNCATED
Source method: isolated from a genetically manipulated source
Details: FAMILY 5 OF GLYCOSYL HYDROLASES / Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Strain: H10 / Gene: CELCCA / Plasmid: PJF118EH / Gene (production host): CELCCA / Production host: Escherichia coli (E. coli) / References: UniProt: P17901, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / pH: 6
Details: CRYSTALS WERE GROWN AT 4 DEGREES C AND PH 6.0, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Roig, V., (1993) J. Mol. Biol., 233, 325.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 mg/mlenzyme1drop
320-23 %(w/v)PEG40001reservoir
450-100 mMsodium citrate1reservoir
2reservoir1drop0.002ml

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X3110.87
SYNCHROTRONEMBL/DESY, HAMBURG BW7B20.998
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATENov 14, 1994
MARRESEARCH2IMAGE PLATE AREA DETECTORNov 17, 1994
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.9981
ReflectionResolution: 1.6→20 Å / Num. obs: 59967 / % possible obs: 98 % / Observed criterion σ(I): 2.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Highest resolution: 1.6 Å / Num. measured all: 355167 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.6→7 Å / σ(F): 2
Details: THE SIDE CHAIN ATOMS OF TRP 181 AND ARG 358 WERE MODELED WITH PARTIAL OCCUPATION OF 0.7. THE SIDE CHAIN ATOMS OF ASN 46 WERE MODELED WITH PARTIAL OCCUPATION OF 0.6.
RfactorNum. reflection% reflection
Rfree0.22 --
Rwork0.191 --
obs0.191 53913 98.8 %
Displacement parametersBiso mean: 17.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 0 0 375 3410
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2315
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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