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- PDB-1g1k: COHESIN MODULE FROM THE CELLULOSOME OF CLOSTRIDIUM CELLULOLYTICUM -

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Basic information

Entry
Database: PDB / ID: 1g1k
TitleCOHESIN MODULE FROM THE CELLULOSOME OF CLOSTRIDIUM CELLULOLYTICUM
ComponentsSCAFFOLDING PROTEIN
KeywordsSTRUCTURAL PROTEIN / Beta -Barrel
Function / homology
Function and homology information


cellulose binding / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / 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 ...Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / 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 / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSpinelli, S. / Fierobe, H.-P. / Belaich, A. / Belaich, J.-P. / Henrissat, B. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of a cohesin module from Clostridium cellulolyticum: implications for dockerin recognition.
Authors: Spinelli, S. / Fierobe, H.P. / Belaich, A. / Belaich, J.P. / Henrissat, B. / Cambillau, C.
History
DepositionOct 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SCAFFOLDING PROTEIN
B: SCAFFOLDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,2972
Polymers29,2972
Non-polymers00
Water4,071226
1
A: SCAFFOLDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,6491
Polymers14,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SCAFFOLDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,6491
Polymers14,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.5, 57.25, 105.72
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsMONOMER, POSSIBLY A DIMER

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Components

#1: Protein SCAFFOLDING PROTEIN / COHESIN-CONTAINING PROTEIN


Mass: 14648.539 Da / Num. of mol.: 2 / Fragment: RESIDUES 287 - 428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Tissue: CELLULOSOME MODULE / Plasmid: PET-COH 1B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q45996
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000 (30%), 150 mM (NH4)2SO4, 100 mM guanidine hydrochloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
230 %(w/v)PEG80001reservoir
3150 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.988
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 24484 / Num. obs: 22829 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / % possible all: 97.8
Reflection
*PLUS
% possible obs: 98 %
Reflection shell
*PLUS
% possible obs: 98.8 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1102 4.2 %RANDOM
Rwork0.23 ---
all0.23 22829 --
obs0.23 22829 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 226 2280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d28.3
X-RAY DIFFRACTIONc_improper_angle_d1.47
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.2 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.47

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