SAXSdb — 2bif

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

PROTEIN (6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-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 1–468 Chain B； UniProt 1–468	Mutation：W15F, W64F, H256A, W299F, W320F	BOG octyl beta-D-glucopyranoside × 3 F6P 6-O-phosphono-beta-D-fructofuranose × 2 MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 SIN SUCCINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；90MM SUCCINATE, PH 6.0, 17% PEG4000, 1% B-OCTYLGLUCOSIDE, 10% GLYCEROL, pH 7.0	Resolution 2.40 Å R-free 0.244

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 2BIF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BIF 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE BIFUNCTIONAL ENZYME COMPLEXED WITH ATP-G-S AND PHOSPHATE Deposited 1996-11-08	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 1–468（468 aa）	Mutation：W15F, W64F, W299F, W320F	MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PROTEIN WAS CRYSTALLISED FROM 50MM SUCCINATE, PH 6.0, 10MM HEPES PH 7.0, 18% PEG 4000, 1% N-OCTYLGLUCOSIDE	Resolution 2.00 Å R-free 0.250
3BIF 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE EMPTY 6-PF-2K ACTIVE SITE Deposited 1999-05-05	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 1–468（468 aa）	Mutation：W15F, W64F, W299F, W320F	BOG octyl beta-D-glucopyranoside × 4 PO4 PHOSPHATE ION × 4 SIN SUCCINIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 50MM SUCCINATE, PH 5.5, 50MM TRIS-PO4, PH 7.5, 11% PEG 4000, 100UM EDTA, 10MM DTT, 10% GLYCEROL, 3MM MGCL2., pH 7.0	Resolution 2.30 Å R-free 0.243

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

View Construct and Data Evidence

UniProt name	F264_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–469； UniProt 1–468 Author chain B； PDBConstruct 1–469； UniProt 1–468

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	2bif
Deposition date deposition_date	1998-10-26
Structure title title	6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE H256A MUTANT WITH F6P IN PHOSPHATASE ACTIVE SITE
Keywords keywords	KINASE, TRANSFERASE (PHOSPHO), PHOSPHATASE, HYDROLASE (PHOSPHO), GLYCOLYSIS, BIFUNCTIONAL ENZYME, TRANSFERASE, HYDROLASE; TRANSFERASE, 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	31.27 Å
Radius of gyration Rg (electron density) rg_electron	30.06 Å
Forward intensity I(0) i0	169483000.00
Molecular weight molecular_weight	102040.0 kDa
Excluded volume excluded_volume	127090 Å³
Envelope volume envelope_volume	156180 Å³
Hydration-shell volume shell_volume	42478 Å³
Envelope diameter envelope_diameter	101.1 Å
Shell Rg shell_rg	37.78 Å
Envelope Rg envelope_rg	30.17 Å
Shape Rg shape_rg	30.07 Å
Total Rg total_rg	30.68 Å
Total atoms total_atoms	7157
Residues n_residues	864
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	96.0 Å
Rg (real space) rg_real	31.09 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	1.6950e+08
I(0) uncertainty (real space) i0_real_error	2.6770e+06
Rg (reciprocal space) rg_reciprocal	31.17 Å
I(0) (reciprocal space) i0_reciprocal	169500000.0000
Solution quality estimate total_estimate	0.9012
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.3 Å
Skewness Skewness skewness	0.121
Kurtosis Kurtosis kurtosis	-0.479
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39950000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.903

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	PROTEIN (6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE)
Molecular weight formula_weight	54001.5 kDa
EC 编号 ec_number	2.7.1.105, 3.1.3.46
Mutation mutation	W15F, W64F, H256A, W299F, W320F
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	7444

MASPRELTQNPLKKIFMPYSNGRPALHASQRGVCMTNCPTLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFNVGQYRRDMVKTYKSFEFFLPDNEEGLKIRKQCALAALNDVRKFLSEEGGHVAVFDATNTTRERRAMIFNFGEQNGYKTFFVESICVDPEVIAANIVQVKLGSPDYVNRDSDEATEDFMRRIECYENSYESLDEEQDRDLSYIKIMDVGQSYVVNRVADHIQSRIVYYLMNIHVTPRSIYLCRAGESELNLKGRIGGDPGLSPRGREFSKHLAQFISDQNIKDLKVFTSQMKRTIQTAEALSVPYEQFKVLNEIDAGVCEEMTYEEIQDHYPLEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKAAEELPYLKCPLHTVLKLTPVAYGCKVESIFLNVAAVNTHRDRPQNVDISRPSEEALVTVPAHQ

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	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	275

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2bifa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.7 — 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain

Domain ID domain_id	d2bifa2
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	d2bifb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.7 — 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain

Domain ID domain_id	d2bifb2
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 (4 domains)

Domain ID domain_id	2bifA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2bifA02
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	2bifB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2bifB02
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 (1)

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Unit-cell length a length_a	61.740 Å
Unit-cell length b length_b	73.510 Å
Unit-cell length c length_c	76.700 Å
Unit-cell angle α angle_alpha	116.90 °
Unit-cell angle β angle_beta	99.31 °
Unit-cell angle γ angle_gamma	105.20 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2440

fit	/app/data/saxs_computation/bi/2bif/2bif.fit
pddf	/app/data/pr_computation/bi/2bif/2bif.pr.out
profile	/app/data/saxs_computation/bi/2bif/2bif.dat

6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE H256A MUTANT WITH F6P IN PHOSPHATASE ACTIVE SITE