11ko

Structure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+

Method: X-RAY DIFFRACTION Dmax: 77.4 Å Quality: GOOD

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

Phosphoenolpyruvate carboxykinase (ATP)

Escherichia coli

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 2–540 Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;4 ul drop with 4 mg/mL protein, 1 mM ADP, 1 mM phosphoenol pyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.5), 200 mM ammonium acetate and 12% PEG 4000 was allowed to equilibrate with a 1 mL reservoir of 100 mM sodium acetate, 200 mM ammonium acetate and 31% PEG 4000 Resolution 1.58 Å R-free 0.185

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 18 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 3–541; UniProt 2–540

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 11ko

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 11ko
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2. Structure Basics 2. Structure Basics

Entry ID entry_id11ko
Deposition date deposition_date2026-03-02
最后修订 last_revision2026-04-29
Structure title titleStructure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+
Keywords keywordsPEPCK, PCKA, adenyl nucleotide binding, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.02
Radius of gyration Rg (electron density) rg_electron22.97
Forward intensity I(0) i058000300.00
Molecular weight molecular_weight59107.0 kDa
Excluded volume excluded_volume73784 ų
Envelope volume envelope_volume85131 ų
Hydration-shell volume shell_volume29838 ų
Envelope diameter envelope_diameter80.9
Shell Rg shell_rg30.97
Envelope Rg envelope_rg23.19
Shape Rg shape_rg22.98
Total Rg total_rg23.79
Total atoms total_atoms4162
Residues n_residues530
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 dmax77.4
Rg (real space) rg_real23.90
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real5.8000e+07
I(0) uncertainty (real space) i0_real_error7.2100e+05
Rg (reciprocal space) rg_reciprocal23.93
I(0) (reciprocal space) i0_reciprocal58000000.0000
Solution quality estimate total_estimate0.8894
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.0
Skewness Skewness skewness0.244
Kurtosis Kurtosis kurtosis-0.343
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18440000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.971

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)