2olq

How Does an Enzyme Recognize CO2?

Method: X-RAY DIFFRACTION Dmax: 82.5 Å Quality: GOOD

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

Phosphoenolpyruvate carboxykinase

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 1–540 Not recorded MN MANGANESE (II) ION × 1 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CO2 CARBON DIOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 4.5;298 K;30% P4000, 0.1 M sodium acetate pH 4.5, 0.2 M ammonium acetate, VAPOR DIFFUSION, temperature 298K Resolution 1.94 Å R-free 0.235

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 PPCK_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 2olq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2olq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2olq
Deposition date deposition_date2007-01-19
Structure title titleHow Does an Enzyme Recognize CO2?
Keywords keywordsphosphoenolpyruvate carboxykinase, CO2, LYASE; LYASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.97
Radius of gyration Rg (electron density) rg_electron22.96
Forward intensity I(0) i058226700.00
Molecular weight molecular_weight59241.0 kDa
Excluded volume excluded_volume73938 ų
Envelope volume envelope_volume85136 ų
Hydration-shell volume shell_volume29868 ų
Envelope diameter envelope_diameter82.8
Shell Rg shell_rg31.06
Envelope Rg envelope_rg23.23
Shape Rg shape_rg22.97
Total Rg total_rg23.80
Total atoms total_atoms4172
Residues n_residues535
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 dmax82.5
Rg (real space) rg_real23.86
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real5.8230e+07
I(0) uncertainty (real space) i0_real_error7.6150e+05
Rg (reciprocal space) rg_reciprocal23.89
I(0) (reciprocal space) i0_reciprocal58230000.0000
Solution quality estimate total_estimate0.8650
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha20920000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2olqa1
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_idd2olqa2
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

CATH v4.4 (3 domains)

Domain ID domain_id2olqA01
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_id2olqA02
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_id2olqA03
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)