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- PDB-1v0a: Family 11 Carbohydrate-Binding Module of cellulosomal cellulase L... -

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Basic information

Entry
Database: PDB / ID: 1v0a
TitleFamily 11 Carbohydrate-Binding Module of cellulosomal cellulase Lic26A-Cel5E of Clostridium thermocellum
ComponentsENDOGLUCANASE H
KeywordsHYDROLASE / CARBOHYDRATE BINDING MODULE / CELLULOSOME / CLOSTRIDIUM THERMOCELLUM / CELLULOSE DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


cellulase / beta-glucosidase activity / cellulase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Galactose-binding lectin / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. ...Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Galactose-binding lectin / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / : / 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) / Galactose-binding-like domain superfamily / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsCarvalho, A.L. / Romao, M.J. / Goyal, A. / Prates, J.A.M. / Pires, V.M.R. / Ferreira, L.M.A. / Bolam, D.N. / Gilbert, H.J. / Fontes, C.M.G.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Family 11 Carbohydrate-Binding Module of Clostridium Thermocellum Lic26A-Cel5E Accomodates Beta-1,4- and Beta-1,3-1,4-Mixed Linked Glucans at a Single Binding Site
Authors: Carvalho, A.L. / Goyal, A. / Prates, J.A.M. / Bolam, D.N. / Gilbert, H.J. / Pires, V.M.R. / Ferreira, L.M.A. / Planas, A. / Romao, M.J. / Fontes, C.M.G.A.
History
DepositionMar 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3465
Polymers20,0731
Non-polymers2724
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.143, 50.892, 40.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ENDOGLUCANASE H / CELLULOSE BINDING PROTEIN A / EGH / ENDO-1 / 4-BETA-GLUCANASE / CELLULASE H


Mass: 20073.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P16218, cellulase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE, LICHENIN AND ...CATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE, LICHENIN AND CEREAL BETA-D-GLUCANS.

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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 Å3/Da / Density % sol: 36.5 %
Crystal growpH: 6 / Details: pH 6.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.981033,0.981266, 0.976315
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9810331
20.9812661
30.9763151
ReflectionResolution: 1.977→24.299 Å / Num. obs: 11449 / % possible obs: 99.5 % / Redundancy: 1.84 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 30.3
Reflection shellResolution: 1.98→2.02 Å / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 8.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.98→19 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.961 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 535 4.8 %RANDOM
Rwork0.193 ---
obs0.195 10598 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--0.35 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 12 182 1527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0211354
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8291.9261835
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021023
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1580.2575
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0710.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2441.5834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.47621335
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8753520
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2584.5500
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.241 40
Rwork0.194 712

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