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1d9q

OXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATASE FORM 1

Method: X-RAY DIFFRACTION Dmax: 112.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

FRUCTOSE-1,6-BISPHOSPHATASE

Pisum sativum

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 Not recorded No other associated polymer 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

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 1D9Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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
1DCU REDOX SIGNALING IN THE CHLOROPLAST: STRUCTURE OF OXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATE PHOSPHATASE Deposited 1999-11-05 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：A197I, E232K Mutation：A197I, E232K Mutation：A197I, E232K Mutation：A197I, E232K No recorded non-water small molecule 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

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 1d9q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d9q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d9q
Deposition date deposition_date1999-10-29
Structure title titleOXIDIZED PEA FRUCTOSE-1,6-BISPHOSPHATASE FORM 1
Keywords keywordsCHLOROPLAST, PHOTOSYNTHESIS, REDOX REGULATION, THIOREDOXIN, ALLOSTERY, DISULFIDE BRIDGE, CALVIN CYCLE, 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_guinier34.91 Å
Radius of gyration Rg (electron density) rg_electron33.91 Å
Forward intensity I(0) i0293233000.00
Molecular weight molecular_weight139830.0 kDa
Excluded volume excluded_volume175500 ų
Envelope volume envelope_volume217780 ų
Hydration-shell volume shell_volume52099 ų
Envelope diameter envelope_diameter112.4 Å
Shell Rg shell_rg41.85 Å
Envelope Rg envelope_rg33.82 Å
Shape Rg shape_rg33.94 Å
Total Rg total_rg34.38 Å
Total atoms total_atoms9850
Residues n_residues1308
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 dmax112.6 Å
Rg (real space) rg_real34.83 Å
Rg uncertainty (real space) rg_real_error0.72 Å
I(0) (real space) i0_real2.9320e+08
I(0) uncertainty (real space) i0_real_error3.8760e+06
Rg (reciprocal space) rg_reciprocal34.88 Å
I(0) (reciprocal space) i0_reciprocal293200000.0000
Solution quality estimate total_estimate0.8950
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.0 Å
Skewness Skewness skewness0.245
Kurtosis Kurtosis kurtosis-0.511
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha268200000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.893
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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_idd1d9qa_
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_idd1d9qb_
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_idd1d9qc_
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_idd1d9qd_
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_id1d9qA01
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_id1d9qA02
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_id1d9qB01
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_id1d9qB02
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_id1d9qC01
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_id1d9qC02
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_id1d9qD01
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_id1d9qD02
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)