1z2v

Crystal Structure of Glu60 deletion Mutant of Human Acidic Fibroblast Growth Factor

Method: X-RAY DIFFRACTION Dmax: 71.6 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 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298.15 K;PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K Resolution 1.90 Å R-free 0.221
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 16–155 Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298.15 K;PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K Resolution 1.90 Å R-free 0.221

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 7–145; UniProt 16–155 Author chain B; PDBConstruct 7–145; 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 1z2v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1z2v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1z2v
Deposition date deposition_date2005-03-09
Structure title titleCrystal Structure of Glu60 deletion Mutant of Human Acidic Fibroblast Growth Factor
Keywords keywordsbeta-trefoil, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.28
Radius of gyration Rg (electron density) rg_electron20.88
Forward intensity I(0) i019002400.00
Molecular weight molecular_weight32288.0 kDa
Excluded volume excluded_volume40030 ų
Envelope volume envelope_volume46888 ų
Hydration-shell volume shell_volume19219 ų
Envelope diameter envelope_diameter73.1
Shell Rg shell_rg26.71
Envelope Rg envelope_rg21.15
Shape Rg shape_rg20.89
Total Rg total_rg21.59
Total atoms total_atoms2274
Residues n_residues272
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 dmax71.6
Rg (real space) rg_real21.31
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real1.9000e+07
I(0) uncertainty (real space) i0_real_error2.5660e+05
Rg (reciprocal space) rg_reciprocal21.30
I(0) (reciprocal space) i0_reciprocal19000000.0000
Solution quality estimate total_estimate0.8620
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.2
Skewness Skewness skewness0.390
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5971000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.964

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1z2va1
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_idd1z2va2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1z2vb1
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_idd1z2vb2
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_id1z2vA00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id1z2vB00
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)