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- PDB-1lf1: Crystal Structure of Cel5 from Alkalophilic Bacillus sp. -

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Basic information

Entry
Database: PDB / ID: 1lf1
TitleCrystal Structure of Cel5 from Alkalophilic Bacillus sp.
ComponentsCel5
KeywordsHYDROLASE / Cellulose degradation
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / 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 ...Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / 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
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsShaw, A. / Bott, R. / Vonrhein, C. / Bricogne, G. / Power, S. / Day, A.G.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: A novel combination of two classic catalytic schemes.
Authors: Shaw, A. / Bott, R. / Vonrhein, C. / Bricogne, G. / Power, S. / Day, A.G.
History
DepositionApr 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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: Cel5


Theoretical massNumber of molelcules
Total (without water)34,5031
Polymers34,5031
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.440, 78.160, 55.050
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 Cel5


Mass: 34502.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pcore3 / Production host: Bacillus subtilis (bacteria) / Keywords: Cel5, Alkalophilic Bacillus sp. / References: UniProt: Q59232, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 295 K / pH: 5.5
Details: 0.5-1.0M ammonium sulfate, 200mM sodium cacodylate, pH 5.5, temperature 295K
Crystal grow
*PLUS
Method: unknown
Details: Naki, D., (1998) Appl. Microb. Biotechnol., 49, 290.

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 32428 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rsym value: 0.077 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→2 Å / Mean I/σ(I) obs: 3.61 / % possible all: 92.4
Reflection
*PLUS
Num. measured all: 139842 / Rmerge(I) obs: 0.077

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Processing

SoftwareName: SHELXL-97 / Classification: refinement
RefinementResolution: 1.7→10 Å / Num. parameters: 9855 / Num. restraintsaints: 9682 / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.2228 -5 %
Rwork0.186 --
all0.1895 32223 -
obs0.1895 30612 97.7 %
Refine analyzeOccupancy sum non hydrogen: 2463
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 0 81 2429
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d0.0261
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELX / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 5 % / Rfactor all: 0.183 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.79
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58

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