5byw

Crystal structure of engineered trifunctional CtCEL5E

Method: X-RAY DIFFRACTION Dmax: 129.4 Å Quality: GOOD

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

Endoglucanase H

Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)

UniProt P16218

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 290–654 Fragment:UNP residues 290-654 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;298 K;50mM sodium acetate, 8% PEG 4000 Resolution 2.60 Å R-free 0.260
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 290–654 Fragment:UNP residues 290-654 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;298 K;50mM sodium acetate, 8% PEG 4000 Resolution 2.60 Å R-free 0.260
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 290–654 Fragment:UNP residues 290-654 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;298 K;50mM sodium acetate, 8% PEG 4000 Resolution 2.60 Å R-free 0.260
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 290–654 Fragment:UNP residues 290-654 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;298 K;50mM sodium acetate, 8% PEG 4000 Resolution 2.60 Å R-free 0.260
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 290–654 Fragment:UNP residues 290-654 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.6;298 K;50mM sodium acetate, 8% PEG 4000 Resolution 2.60 Å R-free 0.260

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.

19 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GUNH_CLOTH
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 39–414; UniProt 290–654 Author chain B; PDBConstruct 39–414; UniProt 290–654 Author chain C; PDBConstruct 39–414; UniProt 290–654 Author chain D; PDBConstruct 39–414; UniProt 290–654 Author chain E; PDBConstruct 39–414; UniProt 290–654

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 5byw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5byw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5byw
Deposition date deposition_date2015-06-11
Structure title titleCrystal structure of engineered trifunctional CtCEL5E
Keywords keywordsCtcel5E, cellulose, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.06
Radius of gyration Rg (electron density) rg_electron37.86
Forward intensity I(0) i0525457000.00
Molecular weight molecular_weight186810.0 kDa
Excluded volume excluded_volume232850 ų
Envelope volume envelope_volume282920 ų
Hydration-shell volume shell_volume61995 ų
Envelope diameter envelope_diameter135.2
Shell Rg shell_rg44.00
Envelope Rg envelope_rg37.73
Shape Rg shape_rg37.82
Total Rg total_rg38.30
Total atoms total_atoms13220
Residues n_residues1596
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax129.4
Rg (real space) rg_real38.13
Rg uncertainty (real space) rg_real_error1.16
I(0) (real space) i0_real5.2550e+08
I(0) uncertainty (real space) i0_real_error8.4700e+06
Rg (reciprocal space) rg_reciprocal38.09
I(0) (reciprocal space) i0_reciprocal525400000.0000
Solution quality estimate total_estimate0.8649
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.2
Skewness Skewness skewness0.453
Kurtosis Kurtosis kurtosis-0.136
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha307000000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.865

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd5bywa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.0 — automated matches
Domain ID domain_idd5bywb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.0 — automated matches
Domain ID domain_idd5bywc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.0 — automated matches
Domain ID domain_idd5bywd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.0 — automated matches
Domain ID domain_idd5bywe_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id5bywA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id5bywB00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id5bywC00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id5bywD00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id5bywE00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases

8. Citations (1)

9. Files and Curves (10)