6at4

E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate

Method: X-RAY DIFFRACTION Dmax: 107.7 Å Quality: GOOD

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

Phosphoenolpyruvate carboxykinase (ATP)

Escherichia coli K-12

UniProt P22259

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–540 Not recorded THJ THIOSULFATE × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate Resolution 1.33 Å R-free 0.151
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–540 Not recorded THJ THIOSULFATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;20% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate Resolution 1.33 Å R-free 0.151

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.

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PCKA_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–540; UniProt 1–540 Author chain B; PDBConstruct 1–540; UniProt 1–540

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 6at4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6at4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6at4
Deposition date deposition_date2017-08-27
Structure title titleE. coli phosphoenolpyruvate carboxykinase bound to thiosulfate
Keywords keywordsNonnative ligand, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.69
Radius of gyration Rg (electron density) rg_electron33.04
Forward intensity I(0) i0210666000.00
Molecular weight molecular_weight116940.0 kDa
Excluded volume excluded_volume146250 ų
Envelope volume envelope_volume176470 ų
Hydration-shell volume shell_volume43789 ų
Envelope diameter envelope_diameter110.6
Shell Rg shell_rg40.54
Envelope Rg envelope_rg32.63
Shape Rg shape_rg33.04
Total Rg total_rg33.56
Total atoms total_atoms16075
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 dmax107.7
Rg (real space) rg_real33.67
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real2.1070e+08
I(0) uncertainty (real space) i0_real_error3.1320e+06
Rg (reciprocal space) rg_reciprocal33.69
I(0) (reciprocal space) i0_reciprocal210700000.0000
Solution quality estimate total_estimate0.8960
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.4
Skewness Skewness skewness0.273
Kurtosis Kurtosis kurtosis-0.620
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha92270000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.898

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6at4a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamilyc.109.1 — PEP carboxykinase N-terminal domain
Family Family familyc.109.1.1 — PEP carboxykinase N-terminal domain
Domain ID domain_idd6at4a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.91 — PEP carboxykinase-like
Superfamily Superfamily superfamilyc.91.1 — PEP carboxykinase-like
Family Family familyc.91.1.1 — PEP carboxykinase C-terminal domain
Domain ID domain_idd6at4b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamilyc.109.1 — PEP carboxykinase N-terminal domain
Family Family familyc.109.1.1 — PEP carboxykinase N-terminal domain
Domain ID domain_idd6at4b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.91 — PEP carboxykinase-like
Superfamily Superfamily superfamilyc.91.1 — PEP carboxykinase-like
Family Family familyc.91.1.1 — PEP carboxykinase C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id6at4A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily10 — Phosphoenolpyruvate Carboxykinase, domain 1
Domain ID domain_id6at4A02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily10 — Phosphoenolpyruvate Carboxykinase, domain 2
Domain ID domain_id6at4A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily20
Domain ID domain_id6at4B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily10 — Phosphoenolpyruvate Carboxykinase, domain 1
Domain ID domain_id6at4B02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily10 — Phosphoenolpyruvate Carboxykinase, domain 2
Domain ID domain_id6at4B03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily20

8. Citations (1)

9. Files and Curves (10)