← Back to search
1l1y

The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome

Method: X-RAY DIFFRACTION Dmax: 156.9 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

cellobiohydrolase

Clostridium thermocellum

UniProt P38686

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–678 Not recorded beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.224
2 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–678 Not recorded beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.224
3 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–678 Not recorded beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.224
4 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 1–678 Not recorded beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.224
5 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 1–678 Not recorded beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.224
6 Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain F； UniProt 1–678 Not recorded beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.40 Å R-free 0.224

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1L1Y Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DAQ SOLUTION STRUCTURE OF THE TYPE I DOCKERIN DOMAIN FROM THE CLOSTRIDIUM THERMOCELLUM CELLULOSOME (MINIMIZED AVERAGE STRUCTURE) Deposited 1999-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 672–741（70 aa） Fragment：TYPE I DOCKERIN DOMAIN (RESIDUES 673-741)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6；328 K；Ionic strength (raw mmCIF value) 100mM KCL；Pressure 1
NMR measurement conditions pH 6；328 K；Ionic strength (raw mmCIF value) 100mM KCL；Pressure 1
NMR sample composition 100MM POTASSIUM CHLORIDE; 20MM CALCIUM CHLORIDE; 90% H2O, 10% D2O
Resolution not provided
1DAV SOLUTION STRUCTURE OF THE TYPE I DOCKERIN DOMAIN FROM THE CLOSTRIDIUM THERMOCELLUM CELLULOSOME (20 STRUCTURES) Deposited 1999-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 672–741（70 aa） Fragment：TYPE I DOCKERIN DOMAIN (RESIDUES 673-741)
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6；328 K；Ionic strength (raw mmCIF value) 100mM KCL；Pressure 1
NMR measurement conditions pH 6；328 K；Ionic strength (raw mmCIF value) 100mM KCL；Pressure 1
NMR sample composition 100MM POTASSIUM CHLORIDE; 20MM CALCIUM CHLORIDE; 90% H2O, 10% D2O
Resolution not provided
1L2A The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome Deposited 2002-02-20 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–678（678 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.226
1L2A The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome Deposited 2002-02-20 Different oligomeric state Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–678（678 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.226
1L2A The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome Deposited 2002-02-20 Different oligomeric state Different structure-quality metrics Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–678（678 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.226
1L2A The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome Deposited 2002-02-20 Different oligomeric state Different structure-quality metrics Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–678（678 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.226
1L2A The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome Deposited 2002-02-20 Different oligomeric state Different structure-quality metrics Assembly 5 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–678（678 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.226
1L2A The Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome Deposited 2002-02-20 Different oligomeric state Different structure-quality metrics Assembly 6 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–678（678 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；22% Ammonium sulphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.226

3 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GUNS_CLOTM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–678； UniProt 1–678 Author chain B； PDBConstruct 1–678； UniProt 1–678 Author chain C； PDBConstruct 1–678； UniProt 1–678 Author chain D； PDBConstruct 1–678； UniProt 1–678 Author chain E； PDBConstruct 1–678； UniProt 1–678 Author chain F； PDBConstruct 1–678； UniProt 1–678

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1l1y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l1y
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1l1y
Deposition date deposition_date2002-02-20
Structure title titleThe Crystal Structure and Catalytic Mechanism of Cellobiohydrolase CelS, the Major Enzymatic Component of the Clostridium thermocellum cellulosome
Keywords keywordsalpha/alpha barrel, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.38 Å
Radius of gyration Rg (electron density) rg_electron48.79 Å
Forward intensity I(0) i02691770000.00
Molecular weight molecular_weight435340.0 kDa
Excluded volume excluded_volume542280 ų
Envelope volume envelope_volume677430 ų
Hydration-shell volume shell_volume110050 ų
Envelope diameter envelope_diameter159.0 Å
Shell Rg shell_rg56.83 Å
Envelope Rg envelope_rg48.09 Å
Shape Rg shape_rg48.80 Å
Total Rg total_rg48.97 Å
Total atoms total_atoms30862
Residues n_residues3852
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax156.9 Å
Rg (real space) rg_real48.98 Å
Rg uncertainty (real space) rg_real_error0.93 Å
I(0) (real space) i0_real2.6920e+09
I(0) uncertainty (real space) i0_real_error4.5470e+07
Rg (reciprocal space) rg_reciprocal49.38 Å
I(0) (reciprocal space) i0_reciprocal2693000000.0000
Solution quality estimate total_estimate0.8837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary68.7 Å
Skewness Skewness skewness0.070
Kurtosis Kurtosis kurtosis-0.500
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha858000000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.911
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1l1ya_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.2 — Cellulases catalytic domain
Domain ID domain_idd1l1yb_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.2 — Cellulases catalytic domain
Domain ID domain_idd1l1yc_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.2 — Cellulases catalytic domain
Domain ID domain_idd1l1yd_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.2 — Cellulases catalytic domain
Domain ID domain_idd1l1ye_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.2 — Cellulases catalytic domain
Domain ID domain_idd1l1yf_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.2 — Cellulases catalytic domain

CATH v4.4 (18 domains)

Domain ID domain_id1l1yA01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1l1yA02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology160 — Endo-1,4-beta-glucanase f; domain 2
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 2
Domain ID domain_id1l1yA03
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology870 — Endo-1,4-beta-glucanase f; domain 3
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 3
Domain ID domain_id1l1yB01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1l1yB02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology160 — Endo-1,4-beta-glucanase f; domain 2
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 2
Domain ID domain_id1l1yB03
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology870 — Endo-1,4-beta-glucanase f; domain 3
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 3
Domain ID domain_id1l1yC01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1l1yC02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology160 — Endo-1,4-beta-glucanase f; domain 2
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 2
Domain ID domain_id1l1yC03
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology870 — Endo-1,4-beta-glucanase f; domain 3
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 3
Domain ID domain_id1l1yD01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1l1yD02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology160 — Endo-1,4-beta-glucanase f; domain 2
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 2
Domain ID domain_id1l1yD03
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology870 — Endo-1,4-beta-glucanase f; domain 3
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 3
Domain ID domain_id1l1yE01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1l1yE02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology160 — Endo-1,4-beta-glucanase f; domain 2
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 2
Domain ID domain_id1l1yE03
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology870 — Endo-1,4-beta-glucanase f; domain 3
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 3
Domain ID domain_id1l1yF01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1l1yF02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology160 — Endo-1,4-beta-glucanase f; domain 2
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 2
Domain ID domain_id1l1yF03
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology870 — Endo-1,4-beta-glucanase f; domain 3
Homologous superfamily homologous superfamily10 — Endo-1,4-beta-glucanase f. Domain 3
▶

8. Citations (1)

▶

9. Files and Curves (10)