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- PDB-1l2a: The Crystal Structure and Catalytic Mechanism of Cellobiohydrolas... -

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Basic information

Entry
Database: PDB / ID: 1l2a
TitleThe Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome
Componentscellobiohydrolase
KeywordsHYDROLASE / alpha/alpha barrel
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (reducing end) / cellulose 1,4-beta-cellobiosidase activity (reducing end) / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain ...Endo-1,4-beta-glucanase f; domain 3 / Endo-1,4-beta-glucanase f. Domain 3 / Endo-1,4-beta-glucanase f; domain 2 / Endo-1,4-beta-glucanase f. Domain 2 / Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Few Secondary Structures / Irregular / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-cellobiose / beta-cellohexaose / Cellulose 1,4-beta-cellobiosidase (reducing end) CelS / Cellulose 1,4-beta-cellobiosidase (reducing end) CelS
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsGuimaraes, B.G. / Souchon, H. / Lytle, B.L. / Wu, J.H.D. / Alzari, P.M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The crystal structure and catalytic mechanism of cellobiohydrolase CelS, the major enzymatic component of the Clostridium thermocellum Cellulosome.
Authors: Guimaraes, B.G. / Souchon, H. / Lytle, B.L. / David Wu, J.H. / Alzari, P.M.
History
DepositionFeb 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cellobiohydrolase
B: cellobiohydrolase
C: cellobiohydrolase
D: cellobiohydrolase
E: cellobiohydrolase
F: cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,82918
Polymers459,8306
Non-polymers7,99912
Water20,7171150
1
A: cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9713
Polymers76,6381
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9713
Polymers76,6381
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9713
Polymers76,6381
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9713
Polymers76,6381
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9713
Polymers76,6381
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: cellobiohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9713
Polymers76,6381
Non-polymers1,3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.027, 207.640, 215.354
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
cellobiohydrolase / CELLULASE SS / ENDOGLUCANASE SS


Mass: 76638.320 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: cels / Plasmid: pTRXFUS / Production host: Escherichia coli (E. coli)
References: UniProt: P38686, UniProt: P0C2S5*PLUS, cellulase
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellohexaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 990.860 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / 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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.2
3100 mMTris-HCl1reservoirpH7.4
420-22 %(w/v)ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 223075 / Num. obs: 223075 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 %
Reflection shellResolution: 2.5→2.59 Å / % possible all: 90.5
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 90.5 % / Rmerge(I) obs: 0.245

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.899 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22577 10814 5 %RANDOM
Rwork0.1809 ---
obs0.18312 206366 95.55 %-
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: 34.902 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20 Å2
2---1.83 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30730 0 534 1150 32414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02132374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.93244243
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46653846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.856154559
X-RAY DIFFRACTIONr_chiral_restr0.1080.24515
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225390
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.215874
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.21680
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6221.519110
X-RAY DIFFRACTIONr_mcangle_it1.209230574
X-RAY DIFFRACTIONr_scbond_it1.819313264
X-RAY DIFFRACTIONr_scangle_it2.9024.513669
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 712
Rwork0.238 14339
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.18312 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.44
LS refinement shell
*PLUS
Rfactor Rfree: 0.247 / Rfactor Rwork: 0.209

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