5cln

Crystal structure of a 4-oxalocrotonate tautomerase mutant at 2.7 Angstrom

Method: X-RAY DIFFRACTION Dmax: 97.7 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 2–58 Chain B; UniProt 2–58 Chain C; UniProt 2–58 Chain D; UniProt 2–58 Chain E; UniProt 2–58 Chain F; UniProt 2–58 Fragment:UNP residues 2-58 Mutation:M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;0.2 M sodium formate, 0.1 M Bis-Tris Propane, 20% PEG 3350 Resolution 2.71 Å R-free 0.263
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 2–58 Chain H; UniProt 2–58 Chain I; UniProt 2–58 Fragment:UNP residues 2-58 Mutation:M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;0.2 M sodium formate, 0.1 M Bis-Tris Propane, 20% PEG 3350 Resolution 2.71 Å R-free 0.263
3 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain J; UniProt 2–58 Chain K; UniProt 2–58 Chain L; UniProt 2–58 Fragment:UNP residues 2-58 Mutation:M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;0.2 M sodium formate, 0.1 M Bis-Tris Propane, 20% PEG 3350 Resolution 2.71 Å R-free 0.263
4 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain J; UniProt 2–58 Chain K; UniProt 2–58 Chain L; UniProt 2–58 Fragment:UNP residues 2-58 Mutation:M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;0.2 M sodium formate, 0.1 M Bis-Tris Propane, 20% PEG 3350 Resolution 2.71 Å R-free 0.263
5 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain J; UniProt 2–58 Chain K; UniProt 2–58 Chain L; UniProt 2–58 Fragment:UNP residues 2-58 Mutation:M45Y, F50A No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;0.2 M sodium formate, 0.1 M Bis-Tris Propane, 20% PEG 3350 Resolution 2.71 Å R-free 0.263

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 63 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 1–57; UniProt 2–58 Author chain B; PDBConstruct 1–57; UniProt 2–58 Author chain C; PDBConstruct 1–57; UniProt 2–58 Author chain D; PDBConstruct 1–57; UniProt 2–58 Author chain E; PDBConstruct 1–57; UniProt 2–58 Author chain F; PDBConstruct 1–57; UniProt 2–58 Author chain G; PDBConstruct 1–57; UniProt 2–58 Author chain H; PDBConstruct 1–57; UniProt 2–58 Author chain I; PDBConstruct 1–57; UniProt 2–58 Author chain J; PDBConstruct 1–57; UniProt 2–58 Author chain K; PDBConstruct 1–57; UniProt 2–58 Author chain L; PDBConstruct 1–57; UniProt 2–58

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 5cln

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5cln
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5cln
Deposition date deposition_date2015-07-16
Structure title titleCrystal structure of a 4-oxalocrotonate tautomerase mutant at 2.7 Angstrom
Keywords keywords4-Oxalocrotonate tautomerase, beta-alpha-beta structural motif, tautomerase superfamily, isomerase; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.63
Radius of gyration Rg (electron density) rg_electron29.70
Forward intensity I(0) i089627600.00
Molecular weight molecular_weight73439.0 kDa
Excluded volume excluded_volume92038 ų
Envelope volume envelope_volume136360 ų
Hydration-shell volume shell_volume38749 ų
Envelope diameter envelope_diameter103.4
Shell Rg shell_rg36.58
Envelope Rg envelope_rg29.56
Shape Rg shape_rg29.70
Total Rg total_rg30.43
Total atoms total_atoms5172
Residues n_residues684
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 dmax97.7
Rg (real space) rg_real30.48
Rg uncertainty (real space) rg_real_error0.60
I(0) (real space) i0_real8.9630e+07
I(0) uncertainty (real space) i0_real_error1.2300e+06
Rg (reciprocal space) rg_reciprocal30.55
I(0) (reciprocal space) i0_reciprocal89630000.0000
Solution quality estimate total_estimate0.8907
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.6
Skewness Skewness skewness0.179
Kurtosis Kurtosis kurtosis-0.430
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7100000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd5clna_
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_idd5clnb_
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_idd5clnc_
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_idd5clnd_
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_idd5clne_
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_idd5clnf_
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_idd5clng_
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_idd5clnh_
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_idd5clni_
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_idd5clnj_
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_idd5clnk_
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_idd5clnl_
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 (12 domains)

Domain ID domain_id5clnA00
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_id5clnB00
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_id5clnC00
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_id5clnD00
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_id5clnE00
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_id5clnF00
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_id5clnG00
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_id5clnH00
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_id5clnI00
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_id5clnJ00
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_id5clnK00
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_id5clnL00
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)