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3bif

6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE EMPTY 6-PF-2K ACTIVE SITE

Method: X-RAY DIFFRACTION Dmax: 81.5 Å Quality: EXCELLENT
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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

UniProt P25114

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 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

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 3BIF 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 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
2BIF 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE H256A MUTANT WITH F6P IN PHOSPHATASE ACTIVE SITE Deposited 1998-10-26 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）
Chain B 1–468（468 aa）
Mutation：W15F, W64F, H256A, W299F, W320F 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

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 1–468； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 3bif

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bif
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bif
Deposition date deposition_date1999-05-05
Structure title title6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE EMPTY 6-PF-2K ACTIVE SITE
Keywords keywordsKINASE, PHOSPHOTRANSFERASE, PHOSPHATASE, HYDROLASE (PHOSPHO), GLYCOLYSIS, BIFUNCTIONAL ENZYME, TRANSFERASE; TRANSFERASE
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_guinier26.29 Å
Radius of gyration Rg (electron density) rg_electron25.19 Å
Forward intensity I(0) i043426800.00
Molecular weight molecular_weight50754.0 kDa
Excluded volume excluded_volume63383 ų
Envelope volume envelope_volume76527 ų
Hydration-shell volume shell_volume25837 ų
Envelope diameter envelope_diameter85.0 Å
Shell Rg shell_rg31.98 Å
Envelope Rg envelope_rg25.20 Å
Shape Rg shape_rg25.19 Å
Total Rg total_rg25.94 Å
Total atoms total_atoms3564
Residues n_residues432
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 dmax81.5 Å
Rg (real space) rg_real26.30 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real4.3430e+07
I(0) uncertainty (real space) i0_real_error4.7420e+05
Rg (reciprocal space) rg_reciprocal26.30 Å
I(0) (reciprocal space) i0_reciprocal43430000.0000
Solution quality estimate total_estimate0.9068
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.8 Å
Skewness Skewness skewness0.282
Kurtosis Kurtosis kurtosis-0.666
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11930000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.991
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3bifa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.7 — 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
Domain ID domain_idd3bifa2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.60 — Phosphoglycerate mutase-like
Superfamily Superfamily superfamilyc.60.1 — Phosphoglycerate mutase-like
Family Family familyc.60.1.4 — 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain

CATH v4.4 (2 domains)

Domain ID domain_id3bifA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3bifA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1240 — Phosphoglycerate mutase-like
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8. Citations (2)

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9. Files and Curves (10)