4x1c

Crystal structure of 4-OT from Pseudomonas putida mt-2 with an enamine adduct on the N-terminal proline at 1.7 Angstrom resolution

Method: X-RAY DIFFRACTION Dmax: 114.0 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 Non-standard monomer:Yes (specific site not provided by mmCIF) NCO COBALT HEXAMMINE(III) × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;Hexaamine cobalt chloride, Bis-Tris Propane, 20% PEG3350, co-crystallised with Acetaldehyde Resolution 1.70 Å R-free 0.227
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 Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;Hexaamine cobalt chloride, Bis-Tris Propane, 20% PEG3350, co-crystallised with Acetaldehyde Resolution 1.70 Å R-free 0.227
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 Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;Hexaamine cobalt chloride, Bis-Tris Propane, 20% PEG3350, co-crystallised with Acetaldehyde Resolution 1.70 Å R-free 0.227

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, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–62; UniProt 2–63 Author chain B; 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 I; PDBConstruct 1–62; UniProt 2–63 Author chain J; 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 C; 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 K; PDBConstruct 1–62; UniProt 2–63 Author chain L; 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 4x1c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4x1c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4x1c
Deposition date deposition_date2014-11-24
Structure title titleCrystal structure of 4-OT from Pseudomonas putida mt-2 with an enamine adduct on the N-terminal proline at 1.7 Angstrom resolution
Keywords keywordsenamine formation, isomerase; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.18
Radius of gyration Rg (electron density) rg_electron32.90
Forward intensity I(0) i0142084000.00
Molecular weight molecular_weight94856.0 kDa
Excluded volume excluded_volume118950 ų
Envelope volume envelope_volume151980 ų
Hydration-shell volume shell_volume40456 ų
Envelope diameter envelope_diameter119.3
Shell Rg shell_rg38.14
Envelope Rg envelope_rg33.02
Shape Rg shape_rg32.89
Total Rg total_rg33.31
Total atoms total_atoms6655
Residues n_residues861
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 dmax114.0
Rg (real space) rg_real33.47
Rg uncertainty (real space) rg_real_error0.97
I(0) (real space) i0_real1.4210e+08
I(0) uncertainty (real space) i0_real_error2.3510e+06
Rg (reciprocal space) rg_reciprocal33.35
I(0) (reciprocal space) i0_reciprocal142100000.0000
Solution quality estimate total_estimate0.8237
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.6
Skewness Skewness skewness0.594
Kurtosis Kurtosis kurtosis-0.090
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21830000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.675; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.752

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

Domain ID domain_idd4x1ca_
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_idd4x1cb_
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_idd4x1cc_
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_idd4x1cd_
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_idd4x1ce_
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_idd4x1cf_
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_idd4x1cg_
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_idd4x1ch_
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_idd4x1ci_
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_idd4x1cj_
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_idd4x1ck_
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_idd4x1cl_
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_idd4x1cm_
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_idd4x1cn_
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_idd4x1co_
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 (15 domains)

Domain ID domain_id4x1cA00
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_id4x1cB00
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_id4x1cC00
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_id4x1cD00
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_id4x1cE00
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_id4x1cF00
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_id4x1cG00
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_id4x1cH00
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_id4x1cI00
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_id4x1cJ00
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_id4x1cK00
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_id4x1cL00
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_id4x1cM00
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_id4x1cN00
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_id4x1cO00
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)