SAXSdb — 1dbz

▼

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

FRUCTOSE-1,6-BISPHOSPHATASE

Pisum sativum

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：C153S	No other associated polymer	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

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 1DBZ	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
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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dbz
Deposition date deposition_date	1999-11-03
Structure title title	C153S MUTANT OF PEA FRUCTOSE-1,6-BISPHOSPHATASE
Keywords keywords	CHLOROPLAST, PHOTOSYNTHESIS, REDOX REGULATION, THIOREDOXIN, ALLOSTERY, DISULFIDE BRIDGE, CALVIN CYCLE, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.65 Å
Radius of gyration Rg (electron density) rg_electron	33.73 Å
Forward intensity I(0) i0	280566000.00
Molecular weight molecular_weight	137370.0 kDa
Excluded volume excluded_volume	172720 Å³
Envelope volume envelope_volume	210940 Å³
Hydration-shell volume shell_volume	50924 Å³
Envelope diameter envelope_diameter	111.7 Å
Shell Rg shell_rg	41.47 Å
Envelope Rg envelope_rg	33.64 Å
Shape Rg shape_rg	33.75 Å
Total Rg total_rg	34.20 Å
Total atoms total_atoms	9686
Residues n_residues	1286
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	111.8 Å
Rg (real space) rg_real	34.59 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	2.8060e+08
I(0) uncertainty (real space) i0_real_error	4.3070e+06
Rg (reciprocal space) rg_reciprocal	34.63 Å
I(0) (reciprocal space) i0_reciprocal	280600000.0000
Solution quality estimate total_estimate	0.8938
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.9 Å
Skewness Skewness skewness	0.267
Kurtosis Kurtosis kurtosis	-0.502
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	273700000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.878

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dbza_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d1dbzb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d1dbzc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

Domain ID domain_id	d1dbzd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.7 — Carbohydrate phosphatase
Superfamily Superfamily superfamily	e.7.1 — Carbohydrate phosphatase
Family Family family	e.7.1.1 — Inositol monophosphatase/fructose-1,6-bisphosphatase-like

CATH v4.4 (8 domains)

Domain ID domain_id	1dbzA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1dbzA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1dbzB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1dbzB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1dbzC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1dbzC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

Domain ID domain_id	1dbzD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Fructose-1,6-Bisphosphatase, subunit A, domain 1

Domain ID domain_id	1dbzD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	80 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	78.900 Å
Unit-cell length b length_b	114.500 Å
Unit-cell length c length_c	94.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2350
R_free r_free	0.2910

Description description	FRUCTOSE-1,6-BISPHOSPHATASE
Molecular weight formula_weight	39226.0 kDa
EC 编号 ec_number	3.1.3.11
Mutation mutation	C153S
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9686

C153S MUTANT OF PEA FRUCTOSE-1,6-BISPHOSPHATASE

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

FRUCTOSE-1,6-BISPHOSPHATASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pisum sativum
通用名 common_name	pea
NCBI Class编号 ncbi_taxonomy_id	3888
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/db/1dbz/1dbz.fit
pddf	/app/data/pr_computation/db/1dbz/1dbz.pr.out
profile	/app/data/saxs_computation/db/1dbz/1dbz.dat