7q04

Crystal structure of TPADO in a substrate-free state

Method: X-RAY DIFFRACTION Dmax: 116.3 Å Quality: GOOD

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

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1

Comamonas sp.

UniProt Q3C1E2

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 1–154 Chain B; UniProt 1–154 Chain C; UniProt 1–154 Not recorded Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 × 3 (Q3C1D5) Lysozyme × 1 (P00698) FES FE2/S2 (INORGANIC) CLUSTER × 3 FE FE (III) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate, 0.1 M buffer Imidazole/MES pH 6.5 Resolution 2.28 Å R-free 0.225

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TPDB1_COMSP
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–154; UniProt 1–154 Author chain B; PDBConstruct 1–154; UniProt 1–154 Author chain C; PDBConstruct 1–154; UniProt 1–154

Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2

Comamonas sp.

UniProt Q3C1D5

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain D; UniProt 1–413 Chain E; UniProt 1–413 Chain F; UniProt 1–413 Not recorded Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1 × 3 (Q3C1E2) Lysozyme × 1 (P00698) FES FE2/S2 (INORGANIC) CLUSTER × 3 FE FE (III) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate, 0.1 M buffer Imidazole/MES pH 6.5 Resolution 2.28 Å R-free 0.225

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TPDA2_COMSP
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 3–415; UniProt 1–413 Author chain E; PDBConstruct 3–415; UniProt 1–413 Author chain F; PDBConstruct 3–415; UniProt 1–413

Lysozyme

OrganismNot specified

UniProt P00698

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 heterocomplex Heteromer Protein × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain H; UniProt 19–147 Not recorded Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1 × 3 (Q3C1E2) Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 × 3 (Q3C1D5) FES FE2/S2 (INORGANIC) CLUSTER × 3 FE FE (III) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate, 0.1 M buffer Imidazole/MES pH 6.5 Resolution 2.28 Å R-free 0.225

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.

1320 other PDB entries and 1450 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 3
Chains and sequence ranges Author chain H; PDBConstruct 1–129; UniProt 19–147

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 7q04

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7q04
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id7q04
Deposition date deposition_date2021-10-14
Structure title titleCrystal structure of TPADO in a substrate-free state
Keywords keywordsterephthalic acid, TPA, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.93
Radius of gyration Rg (electron density) rg_electron35.81
Forward intensity I(0) i0604180000.00
Molecular weight molecular_weight194440.0 kDa
Excluded volume excluded_volume240740 ų
Envelope volume envelope_volume304430 ų
Hydration-shell volume shell_volume67393 ų
Envelope diameter envelope_diameter127.7
Shell Rg shell_rg44.67
Envelope Rg envelope_rg35.64
Shape Rg shape_rg35.80
Total Rg total_rg36.39
Total atoms total_atoms26897
Residues n_residues1741
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 dmax116.3
Rg (real space) rg_real36.68
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real6.0420e+08
I(0) uncertainty (real space) i0_real_error9.8830e+06
Rg (reciprocal space) rg_reciprocal36.84
I(0) (reciprocal space) i0_reciprocal604300000.0000
Solution quality estimate total_estimate0.8901
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.7
Skewness Skewness skewness0.109
Kurtosis Kurtosis kurtosis-0.449
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha115300000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.928

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7q04D01
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id7q04E01
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id7q04F01
Class class2 — Mainly Beta
Architecture architecture102 — 3-layer Sandwich
Topology topology10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily10 — Rieske [2Fe-2S] iron-sulphur domain
Domain ID domain_id7q04H01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)