6at3

E. coli phosphoenolpyruvate carboxykinase Y207F mutant bound to thiosulfate and oxaloacetate

Method: X-RAY DIFFRACTION Dmax: 107.2 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–540 Chain B; UniProt 1–540 Mutation:Y207F OAA OXALOACETATE ION × 1 THJ THIOSULFATE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;24% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate Resolution 1.46 Å R-free 0.219

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 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 6at3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6at3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6at3
Deposition date deposition_date2017-08-27
Structure title titleE. coli phosphoenolpyruvate carboxykinase Y207F mutant bound to thiosulfate and oxaloacetate
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_guinier34.05
Radius of gyration Rg (electron density) rg_electron33.44
Forward intensity I(0) i0207787000.00
Molecular weight molecular_weight116150.0 kDa
Excluded volume excluded_volume145190 ų
Envelope volume envelope_volume177500 ų
Hydration-shell volume shell_volume43467 ų
Envelope diameter envelope_diameter108.8
Shell Rg shell_rg40.92
Envelope Rg envelope_rg32.95
Shape Rg shape_rg33.44
Total Rg total_rg33.97
Total atoms total_atoms16053
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 dmax107.2
Rg (real space) rg_real34.03
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real2.0780e+08
I(0) uncertainty (real space) i0_real_error2.9240e+06
Rg (reciprocal space) rg_reciprocal34.04
I(0) (reciprocal space) i0_reciprocal207800000.0000
Solution quality estimate total_estimate0.8953
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.0
Skewness Skewness skewness0.259
Kurtosis Kurtosis kurtosis-0.665
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha86530000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.828

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd6at3a1
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_idd6at3a2
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_idd6at3a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6at3b1
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_idd6at3b2
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_id6at3A01
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_id6at3A02
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_id6at3A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily20
Domain ID domain_id6at3B01
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_id6at3B02
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_id6at3B03
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)