4gx3

Product Complexes of Porcine Liver Fructose-1,6-bisphosphatase with mutation R22M Reveal a T-state Conformation

Method: X-RAY DIFFRACTION Dmax: 86.5 Å Quality: GOOD

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

Fructose-1,6-bisphosphatase 1

Sus scrofa

UniProt P00636

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–338 Chain B; UniProt 2–338 Mutation:R22M F6P 6-O-phosphono-beta-D-fructofuranose × 4 MG MAGNESIUM ION × 8 PO4 PHOSPHATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:HANGING DROP;pH 7.5;298 K;PEG3350, t-butyl alcohol, glycerol, pH 7.5, HANGING DROP, temperature 298K Resolution 2.25 Å R-free 0.270

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.

66 other PDB entries and 79 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F16P1_PIG
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–337; UniProt 2–338 Author chain B; PDBConstruct 1–337; UniProt 2–338

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 4gx3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gx3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gx3
Deposition date deposition_date2012-09-03
Structure title titleProduct Complexes of Porcine Liver Fructose-1,6-bisphosphatase with mutation R22M Reveal a T-state Conformation
Keywords keywordsallosteric enzymes, cooperativity, oligomerization, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.60
Radius of gyration Rg (electron density) rg_electron25.48
Forward intensity I(0) i083230400.00
Molecular weight molecular_weight72112.0 kDa
Excluded volume excluded_volume90606 ų
Envelope volume envelope_volume105610 ų
Hydration-shell volume shell_volume33592 ų
Envelope diameter envelope_diameter92.0
Shell Rg shell_rg33.63
Envelope Rg envelope_rg25.81
Shape Rg shape_rg25.48
Total Rg total_rg26.31
Total atoms total_atoms5042
Residues n_residues654
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 dmax86.5
Rg (real space) rg_real26.51
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real8.3230e+07
I(0) uncertainty (real space) i0_real_error1.1190e+06
Rg (reciprocal space) rg_reciprocal26.54
I(0) (reciprocal space) i0_reciprocal83230000.0000
Solution quality estimate total_estimate0.8931
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3
Skewness Skewness skewness0.260
Kurtosis Kurtosis kurtosis-0.412
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23060000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4gx3a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamilye.7.1 — Carbohydrate phosphatase
Family Family familye.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like
Domain ID domain_idd4gx3b_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamilye.7.1 — Carbohydrate phosphatase
Family Family familye.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (4 domains)

Domain ID domain_id4gx3A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1
Domain ID domain_id4gx3A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily80
Domain ID domain_id4gx3B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1
Domain ID domain_id4gx3B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily80

8. Citations (1)

9. Files and Curves (10)