6fps

Crystal structure of 4-oxalocrotonate tautomerase triple mutant L8Y/M45Y/F50A

Method: X-RAY DIFFRACTION Dmax: 109.1 Å Quality: GOOD

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

2-hydroxymuconate tautomerase

Pseudomonas putida

UniProt Q01468

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–63 Chain B; UniProt 2–63 Chain C; UniProt 2–63 Chain D; UniProt 2–63 Chain E; UniProt 2–63 Chain F; UniProt 2–63 Mutation:L8Y, M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M bistris-propane HCl, pH 7.0 Resolution 1.90 Å R-free 0.222
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 2–63 Chain H; UniProt 2–63 Chain I; UniProt 2–63 Chain J; UniProt 2–63 Chain K; UniProt 2–63 Chain L; UniProt 2–63 Mutation:L8Y, M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M bistris-propane HCl, pH 7.0 Resolution 1.90 Å R-free 0.222
3 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain M; UniProt 2–63 Chain N; UniProt 2–63 Chain O; UniProt 2–63 Chain P; UniProt 2–63 Chain Q; UniProt 2–63 Chain R; UniProt 2–63 Mutation:L8Y, M45Y, F50A PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M bistris-propane HCl, pH 7.0 Resolution 1.90 Å R-free 0.222

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 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 4OT1_PSEPU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–62; UniProt 2–63 Author chain B; PDBConstruct 1–62; UniProt 2–63 Author chain C; PDBConstruct 1–62; UniProt 2–63 Author chain D; PDBConstruct 1–62; UniProt 2–63 Author chain E; PDBConstruct 1–62; UniProt 2–63 Author chain F; PDBConstruct 1–62; UniProt 2–63 Author chain G; PDBConstruct 1–62; UniProt 2–63 Author chain H; PDBConstruct 1–62; UniProt 2–63 Author chain I; PDBConstruct 1–62; UniProt 2–63 Author chain J; PDBConstruct 1–62; UniProt 2–63 Author chain K; PDBConstruct 1–62; UniProt 2–63 Author chain L; PDBConstruct 1–62; UniProt 2–63 Author chain M; PDBConstruct 1–62; UniProt 2–63 Author chain N; PDBConstruct 1–62; UniProt 2–63 Author chain O; PDBConstruct 1–62; UniProt 2–63 Author chain P; PDBConstruct 1–62; UniProt 2–63 Author chain Q; PDBConstruct 1–62; UniProt 2–63 Author chain R; PDBConstruct 1–62; UniProt 2–63

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 6fps

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6fps
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6fps
Deposition date deposition_date2018-02-12
Structure title titleCrystal structure of 4-oxalocrotonate tautomerase triple mutant L8Y/M45Y/F50A
Keywords keywords2-hydroxymuconate tautomerase, isomerase; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.12
Radius of gyration Rg (electron density) rg_electron33.29
Forward intensity I(0) i0215557000.00
Molecular weight molecular_weight116080.0 kDa
Excluded volume excluded_volume145120 ų
Envelope volume envelope_volume187000 ų
Hydration-shell volume shell_volume46692 ų
Envelope diameter envelope_diameter110.4
Shell Rg shell_rg40.22
Envelope Rg envelope_rg32.78
Shape Rg shape_rg33.29
Total Rg total_rg33.85
Total atoms total_atoms8177
Residues n_residues1069
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 dmax109.1
Rg (real space) rg_real34.04
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real2.1560e+08
I(0) uncertainty (real space) i0_real_error3.2330e+06
Rg (reciprocal space) rg_reciprocal34.09
I(0) (reciprocal space) i0_reciprocal215600000.0000
Solution quality estimate total_estimate0.8997
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.9
Skewness Skewness skewness0.225
Kurtosis Kurtosis kurtosis-0.554
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39610000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

Domain ID domain_idd6fpsa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpse_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsi_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsk_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsl_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsm_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsn_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpso_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsp_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsq_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like
Domain ID domain_idd6fpsr_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.80 — Tautomerase/MIF
Superfamily Superfamily superfamilyd.80.1 — Tautomerase/MIF
Family Family familyd.80.1.1 — 4-oxalocrotonate tautomerase-like

CATH v4.4 (18 domains)

Domain ID domain_id6fpsA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsJ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsL00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsM00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsN00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsO00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsP00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsQ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor
Domain ID domain_id6fpsR00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily10 — Macrophage Migration Inhibitory Factor

8. Citations (1)

9. Files and Curves (10)