6asi

E. coli phosphoenolpyruvate carboxykinase G209S mutant bound to methanesulfonate

Method: X-RAY DIFFRACTION Dmax: 83.9 Å Quality: REASONABLE

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

Phosphoenolpyruvate carboxykinase (ATP)

Escherichia coli (strain K12)

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 Mutation:G209S ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 03S methanesulfonic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;16% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.3 M sodium chloride, 0.1 M sodium methanesulfonate Resolution 1.79 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 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 6asi

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6asi
Deposition date deposition_date2017-08-24
Structure title titleE. coli phosphoenolpyruvate carboxykinase G209S mutant bound to methanesulfonate
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_guinier23.80
Radius of gyration Rg (electron density) rg_electron22.80
Forward intensity I(0) i055027000.00
Molecular weight molecular_weight57560.0 kDa
Excluded volume excluded_volume71690 ų
Envelope volume envelope_volume81953 ų
Hydration-shell volume shell_volume29015 ų
Envelope diameter envelope_diameter79.4
Shell Rg shell_rg30.68
Envelope Rg envelope_rg23.06
Shape Rg shape_rg22.80
Total Rg total_rg23.67
Total atoms total_atoms7923
Residues n_residues529
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 dmax83.9
Rg (real space) rg_real24.56
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real5.4830e+07
I(0) uncertainty (real space) i0_real_error6.6840e+05
Rg (reciprocal space) rg_reciprocal23.73
I(0) (reciprocal space) i0_reciprocal55030000.0000
Solution quality estimate total_estimate0.6618
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.475
Kurtosis Kurtosis kurtosis0.128
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha4.4420
Highest regularization parameter α highest_alpha20550000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.751; Stabil: 0.908; Sysdev: 0.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.681

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd6asia1
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_idd6asia2
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_idd6asia3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id6asiA01
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_id6asiA02
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_id6asiA03
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)