7xy9

Cryo-EM structure of secondary alcohol dehydrogenases TbSADH after carrier-free immobilization based on weak intermolecular interactions

Method: ELECTRON MICROSCOPY Dmax: 101.1 Å Quality: GOOD

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

NADP-dependent isopropanol dehydrogenase

Thermoanaerobacter brockii

UniProt P14941

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–352 Chain B; UniProt 2–352 Chain C; UniProt 2–352 Chain D; UniProt 2–352 Mutation:I86N ZN ZINC ION × 4 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.12 Å

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.

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADH_THEBR
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 8–358; UniProt 2–352 Author chain B; PDBConstruct 8–358; UniProt 2–352 Author chain C; PDBConstruct 8–358; UniProt 2–352 Author chain D; PDBConstruct 8–358; UniProt 2–352

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 7xy9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7xy9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7xy9
Deposition date deposition_date2022-06-01
Structure title titleCryo-EM structure of secondary alcohol dehydrogenases TbSADH after carrier-free immobilization based on weak intermolecular interactions
Keywords keywordsCoordination complex, Activity, Stability, Enzyme Immobilization, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier33.12
Radius of gyration Rg (electron density) rg_electron32.60
Forward intensity I(0) i0325988000.00
Molecular weight molecular_weight148140.0 kDa
Excluded volume excluded_volume186670 ų
Envelope volume envelope_volume224860 ų
Hydration-shell volume shell_volume55366 ų
Envelope diameter envelope_diameter102.9
Shell Rg shell_rg41.09
Envelope Rg envelope_rg32.38
Shape Rg shape_rg32.64
Total Rg total_rg33.09
Total atoms total_atoms10388
Residues n_residues1376
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 dmax101.1
Rg (real space) rg_real32.86
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real3.2600e+08
I(0) uncertainty (real space) i0_real_error4.7510e+06
Rg (reciprocal space) rg_reciprocal32.97
I(0) (reciprocal space) i0_reciprocal326000000.0000
Solution quality estimate total_estimate0.8309
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.1
Skewness Skewness skewness0.105
Kurtosis Kurtosis kurtosis-0.564
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha146800000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7xy9A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id7xy9B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id7xy9C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id7xy9D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain

8. Citations (1)

9. Files and Curves (10)