3fje

Crystal structure of C83S mutant of Human acidic fibroblast growth factor

Method: X-RAY DIFFRACTION Dmax: 69.2 Å Quality: GOOD

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

Heparin-binding growth factor 1

Homo sapiens

UniProt P05230

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 16–155 Mutation:C83S SO4 SULFATE ION × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;3.0M Na formate, 0.4M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.235
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 16–155 Mutation:C83S FMT FORMIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;3.0M Na formate, 0.4M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.235

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.

96 other PDB entries and 216 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 7–146; UniProt 16–155 Author chain B; PDBConstruct 7–146; UniProt 16–155

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 3fje

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3fje
Deposition date deposition_date2008-12-14
Structure title titleCrystal structure of C83S mutant of Human acidic fibroblast growth factor
Keywords keywords;beta-trefoil, Acetylation, Angiogenesis, Developmental protein, Differentiation, Growth factor, Heparin-binding, Mitogen, Polymorphism, HORMONE ;; HORMONE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.15
Radius of gyration Rg (electron density) rg_electron20.69
Forward intensity I(0) i018763500.00
Molecular weight molecular_weight32409.0 kDa
Excluded volume excluded_volume40305 ų
Envelope volume envelope_volume46289 ų
Hydration-shell volume shell_volume19162 ų
Envelope diameter envelope_diameter69.8
Shell Rg shell_rg26.47
Envelope Rg envelope_rg20.89
Shape Rg shape_rg20.69
Total Rg total_rg21.41
Total atoms total_atoms2289
Residues n_residues274
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax69.2
Rg (real space) rg_real21.16
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real1.8760e+07
I(0) uncertainty (real space) i0_real_error2.6650e+05
Rg (reciprocal space) rg_reciprocal21.16
I(0) (reciprocal space) i0_reciprocal18760000.0000
Solution quality estimate total_estimate0.8778
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.4
Skewness Skewness skewness0.369
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5558000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.964

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3fjea1
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3fjea2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3fjeb1
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3fjeb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id3fjeA00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3fjeB00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50

8. Citations (1)

9. Files and Curves (10)