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1dcu

REDOX SIGNALING IN THE CHLOROPLAST: STRUCTURE OF OXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATE PHOSPHATASE

Method: X-RAY DIFFRACTION Dmax: 108.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

FRUCTOSE-1,6-BISPHOSPHATASE

OrganismNot specified

UniProt P46275

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 51–407 Chain B； UniProt 51–407 Chain C； UniProt 51–407 Chain D； UniProt 51–407 Mutation：A197I, E232K No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；PEG 400, Na acetate, magnesium chloride, fructose-6-phosphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.20 Å R-free 0.247

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 1DCU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D9Q OXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATASE FORM 1 Deposited 1999-10-29 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 51–407（357 aa）
Chain B 51–407（357 aa）
Chain C 51–407（357 aa）
Chain D 51–407（357 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；25% PEG 400, 50MM NA ACETATE (PH 5.5), 50MM MGCL2, 5MM F6P, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.40 Å R-free 0.236
1DBZ C153S MUTANT OF PEA FRUCTOSE-1,6-BISPHOSPHATASE Deposited 1999-11-03 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 51–407（357 aa）
Chain B 51–407（357 aa）
Chain C 51–407（357 aa）
Chain D 51–407（357 aa）
Mutation：C153S Mutation：C153S Mutation：C153S Mutation：C153S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；20% PEG 1000, 50MM NA ACETATE (PH 5), 50 MM MGCL2, 5MM F6P, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.65 Å R-free 0.291

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F16P_PEA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–357； UniProt 51–407 Author chain B； PDBConstruct 1–357； UniProt 51–407 Author chain C； PDBConstruct 1–357； UniProt 51–407 Author chain D； PDBConstruct 1–357； UniProt 51–407

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 1dcu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dcu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dcu
Deposition date deposition_date1999-11-05
Structure title titleREDOX SIGNALING IN THE CHLOROPLAST: STRUCTURE OF OXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATE PHOSPHATASE
Keywords keywordsCHLOROPLAST, PHOTOSYNTHESIS, REDOX REGULATION, THIOREDOXIN, ALLOSTERY, HYDROLASE; 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_guinier34.60 Å
Radius of gyration Rg (electron density) rg_electron33.60 Å
Forward intensity I(0) i0296360000.00
Molecular weight molecular_weight140640.0 kDa
Excluded volume excluded_volume176500 ų
Envelope volume envelope_volume211760 ų
Hydration-shell volume shell_volume51296 ų
Envelope diameter envelope_diameter110.7 Å
Shell Rg shell_rg41.49 Å
Envelope Rg envelope_rg33.51 Å
Shape Rg shape_rg33.63 Å
Total Rg total_rg34.06 Å
Total atoms total_atoms9907
Residues n_residues1306
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 dmax108.4 Å
Rg (real space) rg_real34.53 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real2.9640e+08
I(0) uncertainty (real space) i0_real_error4.6700e+06
Rg (reciprocal space) rg_reciprocal34.57 Å
I(0) (reciprocal space) i0_reciprocal296400000.0000
Solution quality estimate total_estimate0.8877
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.1 Å
Skewness Skewness skewness0.251
Kurtosis Kurtosis kurtosis-0.509
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha230900000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.707
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1dcua_
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_idd1dcub_
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_idd1dcuc_
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_idd1dcud_
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 (8 domains)

Domain ID domain_id1dcuA01
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_id1dcuA02
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_id1dcuB01
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_id1dcuB02
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_id1dcuC01
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_id1dcuC02
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_id1dcuD01
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_id1dcuD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily80 —
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8. Citations (1)

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9. Files and Curves (10)