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- PDB-1anu: COHESIN-2 DOMAIN OF THE CELLULOSOME FROM CLOSTRIDIUM THERMOCELLUM -

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Basic information

Entry
Database: PDB / ID: 1anu
TitleCOHESIN-2 DOMAIN OF THE CELLULOSOME FROM CLOSTRIDIUM THERMOCELLUM
ComponentsCOHESIN-2
KeywordsCOHESIN / SCAFFOLDING / CELLULOSE DIGESTION / BETA SANDWICH / THERMOPHILE
Function / homology
Function and homology information


cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / extracellular region
Similarity search - Function
Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Carboxypeptidase-like, regulatory domain superfamily / Clostridium cellulosome enzymes repeated domain signature. ...Immunoglobulin-like - #680 / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Carboxypeptidase-like, regulatory domain superfamily / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellulosomal-scaffolding protein A
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.15 Å
AuthorsShimon, L.J.W. / Yaron, S. / Shoham, Y. / Lamed, R. / Morag, E. / Bayer, E.A. / Frolow, F.
Citation
Journal: Structure / Year: 1997
Title: A cohesin domain from Clostridium thermocellum: the crystal structure provides new insights into cellulosome assembly.
Authors: Shimon, L.J. / Bayer, E.A. / Morag, E. / Lamed, R. / Yaron, S. / Shoham, Y. / Frolow, F.
#1: Journal: FEBS Lett. / Year: 1995
Title: Expression, Purification and Subunit-Binding Properties of Cohesins 2 and 3 of the Clostridium Thermocellum Cellulosome
Authors: Yaron, S. / Morag, E. / Bayer, E.A. / Lamed, R. / Shoham, Y.
#2: Journal: Trends Biotechnol. / Year: 1994
Title: The Cellulosome--A Treasure-Trove for Biotechnology
Authors: Bayer, E.A. / Morag, E. / Lamed, R.
History
DepositionJul 19, 1996Processing site: BNL
Revision 1.0Jul 23, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COHESIN-2


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water43224
1
A: COHESIN-2

A: COHESIN-2


Theoretical massNumber of molelcules
Total (without water)29,5052
Polymers29,5052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)79.509, 47.862, 51.130
Angle α, β, γ (deg.)90.00, 126.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein COHESIN-2


Mass: 14752.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INCORPORATES CELLULOLYTIC ENZYME INTO THE SCAFFOLDING PROTEIN OF CELLULOSOME
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: YS / Cellular location: EXOCELLULAR PROTUBERANCE / Gene: CIPA (CIPB) / Organelle: CELLULOSOME / Plasmid: PQE-COH2/PREP4 / Cellular location (production host): CYTOPLASM / Gene (production host): 6XHIS-COH2 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 BLUE / References: UniProt: Q06851
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51 %
Crystal growpH: 8.6 / Details: 28% PEG 6000, 750 MM LICL, 100 MM TRIS-HCL, PH 8.6
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlprotein1drop
228 %(w/v)PEG60001reservoir
30.75 M1reservoirLiCl
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 8276 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 31.25
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.283 / % possible all: 84
Reflection
*PLUS
Num. measured all: 42676
Reflection shell
*PLUS
% possible obs: 84 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.15→30 Å / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.197 / Rfactor obs: 0.197
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1324 0 0 24 1348
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_deg1.467
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.34
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.056
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
LS refinement shellHighest resolution: 2.15 Å / Rfactor Rfree: 0.369 / Rfactor Rwork: 0.351
Software
*PLUS
Name: X-PLOR / Version: 3.1 / 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_deg26.34
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.056
LS refinement shell
*PLUS
Rfactor obs: 0.351

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