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3eps

The crystal structure of isocitrate dehydrogenase kinase/phosphatase from E. coli

Method: X-RAY DIFFRACTION Dmax: 113.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isocitrate dehydrogenase kinase/phosphatase

Escherichia coli O157:H7

UniProt Q8X607

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 2–578 Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；12% PEG8000, 0.2M magnesium chloride, 0.1M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.268
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–578 Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；12% PEG8000, 0.2M magnesium chloride, 0.1M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.268

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.

Other PDB Difference from Current Entry 3EPS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4P69 Acek (D477A) ICDH complex Deposited 2014-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 4–571（568 aa） Fragment：residues 4-571
Chain B 4–571（568 aa） Fragment：residues 4-571
Mutation：D477A Mutation：D477A AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2mM DTT, 10% glycerol, 0.1M MES pH 6.0, 25%~30% PEG 300
Resolution 3.30 Å R-free 0.247

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACEK_ECO57
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–578； UniProt 2–578 Author chain B； PDBConstruct 2–578； UniProt 2–578

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 3eps

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3eps
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3eps
Deposition date deposition_date2008-09-29
Structure title titleThe crystal structure of isocitrate dehydrogenase kinase/phosphatase from E. coli
Keywords keywords;kinase phosphatase, ATP-binding, Glyoxylate bypass, Kinase, Nucleotide-binding, Protein phosphatase, Tricarboxylic acid cycle, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, transferase, hydrolase ;; transferase, hydrolase
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.59 Å
Radius of gyration Rg (electron density) rg_electron34.24 Å
Forward intensity I(0) i0272620000.00
Molecular weight molecular_weight133430.0 kDa
Excluded volume excluded_volume166950 ų
Envelope volume envelope_volume209750 ų
Hydration-shell volume shell_volume50395 ų
Envelope diameter envelope_diameter115.8 Å
Shell Rg shell_rg41.50 Å
Envelope Rg envelope_rg33.92 Å
Shape Rg shape_rg34.25 Å
Total Rg total_rg34.70 Å
Total atoms total_atoms9417
Residues n_residues1125
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax113.2 Å
Rg (real space) rg_real34.52 Å
Rg uncertainty (real space) rg_real_error0.75 Å
I(0) (real space) i0_real2.7260e+08
I(0) uncertainty (real space) i0_real_error4.5430e+06
Rg (reciprocal space) rg_reciprocal34.57 Å
I(0) (reciprocal space) i0_reciprocal272600000.0000
Solution quality estimate total_estimate0.8942
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.9 Å
Skewness Skewness skewness0.279
Kurtosis Kurtosis kurtosis-0.431
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha87550000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.956
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)