SAXSdb — 1tip

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

PHOSPHOENZYME INTERMEDIATE OF FRU-2,6-BISPHOSPHATASE

Rattus norvegicus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 251–440 Chain B； UniProt 251–440	Mutation：30 C-TERMINAL AMINO ACIDS DELETED Non-standard monomer：Yes (specific site not provided by mmCIF)	F6P 6-O-phosphono-beta-D-fructofuranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：A CATALYTIC PHOSPHOSENZYME INTERMEDIATE STATE OF THE BISPHOSPHATASE WAS PREPARED BY SOAKING OF THE NATIVE CRYSTAL OF THE PROTEIN AND TRAPPED USING THE CRYOGENIC DEVICE. A 2.2 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE INTERMEDIATE WAS DETERMINED. A PHOSPHORYLATED CATALYTIC HISTIDINE WAS VISUALIZED ALONG WITH THE FIRST PRODUCT, FRUCTOSE-6 - PHOSPHATE, AND THE CATALYTIC WATER, SHOWING THE COMPREHENSIVE GEOMETRY OF A TRIGONAL BI-PYRAMIDAL STRUCTURE.	Resolution 2.20 Å R-free 0.286

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 1TIP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C7Z REGULATORY COMPLEX OF FRUCTOSE-2,6-BISPHOSPHATASE Deposited 2000-04-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 251–440（190 aa） Chain B 251–440（190 aa）	Not recorded	PO4 PHOSPHATE ION × 2 G3H GLYCERALDEHYDE-3-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.25；293 K；PEG 4000, sodium chloride, Hepes, pH 7.25, EVAPORATION, temperature 293.0K	Resolution 2.60 Å R-free 0.253
1C80 REGULATORY COMPLEX OF FRUCTOSE-2,6-BISPHOSPHATASE Deposited 2000-04-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 251–440（190 aa） Chain B 251–440（190 aa）	Not recorded	PO4 PHOSPHATE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.25；293 K；PEG 4000, sodium chloride, Hepes, pH 7.25, EVAPORATION, temperature 293.0K	Resolution 2.20 Å R-free 0.265
1C81 MICHAELIS COMPLEX OF FRUCTOSE-2,6-BISPHOSPHATASE Deposited 2000-04-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 251–440（190 aa）	Not recorded	FDQ 2,5-anhydro-1-deoxy-1-phosphono-6-O-phosphono-D-glucitol × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.25；293 K；PEG 4000, sodium chloride, Hepes, pH 7.25, EVAPORATION, temperature 293.0K	Resolution 2.50 Å R-free 0.287
1FBT THE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE Deposited 1996-03-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 251–440（190 aa） Chain B 251–440（190 aa）	Mutation：30 AMINO ACIDS DELETED FROM THE C-TERMINAL Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：30 AMINO ACIDS DELETED FROM THE C-TERMINAL Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.278

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F261_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–191； UniProt 251–440 Author chain B； PDBConstruct 2–191； UniProt 251–440

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1tip
Deposition date deposition_date	1997-05-28
Structure title title	THE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE
Keywords keywords	MULTIFUNCTIONAL ENZYME, TRANSFERASE, KINASE, ATP-BINDING, PHOSPHORYLATION, ALTERNATIVE SPLICING, MULTIGENE FAMILY, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.94 Å
Radius of gyration Rg (electron density) rg_electron	23.60 Å
Forward intensity I(0) i0	35510400.00
Molecular weight molecular_weight	44977.0 kDa
Excluded volume excluded_volume	55924 Å³
Envelope volume envelope_volume	66396 Å³
Hydration-shell volume shell_volume	24344 Å³
Envelope diameter envelope_diameter	84.1 Å
Shell Rg shell_rg	30.17 Å
Envelope Rg envelope_rg	23.83 Å
Shape Rg shape_rg	23.60 Å
Total Rg total_rg	24.37 Å
Total atoms total_atoms	3150
Residues n_residues	380
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

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

Maximum dimension Dmax dmax	82.5 Å
Rg (real space) rg_real	24.08 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	3.5510e+07
I(0) uncertainty (real space) i0_real_error	5.4970e+05
Rg (reciprocal space) rg_reciprocal	24.05 Å
I(0) (reciprocal space) i0_reciprocal	35510000.0000
Solution quality estimate total_estimate	0.8427
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.559
Kurtosis Kurtosis kurtosis	-0.087
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10870000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.891; Smooth: 0.923

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PHOSPHOENZYME INTERMEDIATE OF FRU-2,6-BISPHOSPHATASE
Molecular weight formula_weight	22258.3 kDa
EC 编号 ec_number	3.1.3.46
Mutation mutation	30 C-TERMINAL AMINO ACIDS DELETED
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3434

MRSIYLCRHGESELNLRGRIGGDSGLSARGKQYAYALANFIRSQGISSLKVWTSHMKRTIQTAEALGVPYEQWKALNEIDAGVCEEMTYEEIQEHYPEEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKSSDELPYLKCPLHTVLKLTPVAYGCRVESIYLNV

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	6-O-phosphono-beta-D-fructofuranose
Molecular weight formula_weight	260.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	284

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1tipa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.4 — 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain

Domain ID domain_id	d1tipb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamily	c.60.1 — Phosphoglycerate mutase-like
Family Family family	c.60.1.4 — 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain

CATH v4.4 (2 domains)

Domain ID domain_id	1tipA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	1tipB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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8. Citations (3)

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Unit-cell length a length_a	48.230 Å
Unit-cell length b length_b	56.520 Å
Unit-cell length c length_c	90.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2860

fit	/app/data/saxs_computation/ti/1tip/1tip.fit
pddf	/app/data/pr_computation/ti/1tip/1tip.pr.out
profile	/app/data/saxs_computation/ti/1tip/1tip.dat

THE BISPHOSPHATASE DOMAIN OF THE BIFUNCTIONAL RAT LIVER 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE

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

PHOSPHOENZYME INTERMEDIATE OF FRU-2,6-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