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3lc6

The alternative conformation structure of isocitrate dehydrogenase kinase/phosphatase from E. Coli

Method: X-RAY DIFFRACTION Dmax: 113.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isocitrate dehydrogenase kinase/phosphatase

Escherichia coli

UniProt B5Z0A8

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–579 Chain B； UniProt 2–579 Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；295 K；12% PEG 8000, 0.001M calcium chloride, 0.2M magnesium chloride, 0.1M MES 15% Glycerol, 0.002M DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 3.10 Å R-free 0.332
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–579 Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；295 K；12% PEG 8000, 0.001M calcium chloride, 0.2M magnesium chloride, 0.1M MES 15% Glycerol, 0.002M DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 3.10 Å R-free 0.332
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–579 Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；295 K；12% PEG 8000, 0.001M calcium chloride, 0.2M magnesium chloride, 0.1M MES 15% Glycerol, 0.002M DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 3.10 Å R-free 0.332

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 3LC6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LCB The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli. Deposited 2010-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–578（578 aa）
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 6；295 K；25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.222
3LCB The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli. Deposited 2010-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–578（578 aa）
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 6；295 K；25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.222
3LCB The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli. Deposited 2010-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–578（578 aa）
Chain B 1–578（578 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.222

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACEK_ECO5E
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–578； UniProt 2–579 Author chain B； PDBConstruct 1–578； UniProt 2–579

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 3lc6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3lc6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3lc6
Deposition date deposition_date2010-01-09
Structure title titleThe alternative conformation 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, NADP, 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_guinier34.97 Å
Radius of gyration Rg (electron density) rg_electron34.34 Å
Forward intensity I(0) i0248151000.00
Molecular weight molecular_weight127880.0 kDa
Excluded volume excluded_volume160410 ų
Envelope volume envelope_volume208030 ų
Hydration-shell volume shell_volume49969 ų
Envelope diameter envelope_diameter122.5 Å
Shell Rg shell_rg41.13 Å
Envelope Rg envelope_rg34.55 Å
Shape Rg shape_rg34.31 Å
Total Rg total_rg34.91 Å
Total atoms total_atoms9031
Residues n_residues1086
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 dmax113.4 Å
Rg (real space) rg_real34.99 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real2.4820e+08
I(0) uncertainty (real space) i0_real_error3.9750e+06
Rg (reciprocal space) rg_reciprocal34.98 Å
I(0) (reciprocal space) i0_reciprocal248100000.0000
Solution quality estimate total_estimate0.8783
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.3 Å
Skewness Skewness skewness0.394
Kurtosis Kurtosis kurtosis-0.292
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha86030000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.741
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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)