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5ssy

Crystal Structure of human formylglycine generating enzyme

Method: X-RAY DIFFRACTION Dmax: 60.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Formylglycine-generating enzyme

Homo sapiens

UniProt Q8NBK3

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 73–374 Not recorded CU1 COPPER (I) ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 UG6 methyl N-acetyl-L-cysteinate × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9.6 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8.5, 20-25% PEG4000, 0.2-0.3M CaCl2 Resolution 1.29 Å R-free 0.237

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 5SSY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1Y1E human formylglycine generating enzyme Deposited 2004-11-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 73–374（302 aa） Fragment：residues 73-383
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Tris/HCl, CaCl2, PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.73 Å R-free 0.242
2AFT Formylglycine generating enzyme C336S mutant Deposited 2005-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain X 86–371（286 aa） Fragment：residues 86-371
Mutation：C336S CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.66 Å R-free 0.187
2AFY Formylglycine generating enzyme C341S mutant Deposited 2005-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain X 86–371（286 aa） Fragment：residues 86-371
Mutation：C341S Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.49 Å R-free 0.171
2AII wild-type Formylglycine generating enzyme reacted with iodoacetamide Deposited 2005-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain X 86–371（286 aa） Fragment：residues 86-371
Not recorded CA CALCIUM ION × 2 ACM ACETAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.54 Å R-free 0.176
2AIJ Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide CTPSR Deposited 2005-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 86–371（286 aa） Fragment：residues 86-371
Mutation：C336S CA CALCIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.55 Å R-free 0.178
2AIK Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide LCTPSRA Deposited 2005-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 86–371（286 aa） Fragment：residues 86-371
Mutation：C336S CA CALCIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.73 Å R-free 0.174
2HI8 human formylglycine generating enzyme, C336S mutant, bromide co-crystallization Deposited 2006-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 86–371（286 aa） Fragment：RESIDUES 86-371
Mutation：C336S BR BROMIDE ION × 15 CA CALCIUM ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.64 Å R-free 0.191
2HIB human formylglycine generating enzyme, C336S mutant, iodide co-crystallization Deposited 2006-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain X 86–371（286 aa） Fragment：RESIDUES 86-371
Mutation：C336S CA CALCIUM ION × 2 IOD IODIDE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, Calcium iodide, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.238
5SSX Crystal Structure human formylglycine generating enzyme E130D mutant Deposited 2022-08-12 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 73–374（302 aa）
Mutation：E130D CU1 COPPER (I) ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9.6 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8.5, 20-25% PEG4000, 0.2-0.3M CaCl2
Resolution 1.02 Å R-free 0.138
5SSZ Crystal Structure of wild-type human formylglycine generating enzyme bound to Cu(I) Deposited 2022-08-12 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 73–374（302 aa）
Not recorded CU1 COPPER (I) ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9.6 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8.5, 20-25% PEG4000, 0.2-0.3M CaCl2
Resolution 1.02 Å R-free 0.142
8ARU Crystal Structure of human formylglycine generating enzyme Deposited 2022-08-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 73–374（302 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；7-8 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8-9, 20-25% PEG4000, 0.25M CaCl2
Resolution 1.08 Å R-free 0.174

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SUMF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 10–311； UniProt 73–374

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 5ssy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ssy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ssy
Deposition date deposition_date2022-08-12
Structure title titleCrystal Structure of human formylglycine generating enzyme
Keywords keywordsFORMYLGLYCINE, MULTIPLE SULFATASE DEFICIENCY, COPPER, OXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier18.49 Å
Radius of gyration Rg (electron density) rg_electron17.58 Å
Forward intensity I(0) i018546100.00
Molecular weight molecular_weight31587.0 kDa
Excluded volume excluded_volume38904 ų
Envelope volume envelope_volume43460 ų
Hydration-shell volume shell_volume19951 ų
Envelope diameter envelope_diameter58.3 Å
Shell Rg shell_rg24.53 Å
Envelope Rg envelope_rg17.98 Å
Shape Rg shape_rg17.57 Å
Total Rg total_rg18.55 Å
Total atoms total_atoms2224
Residues n_residues277
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 dmax60.3 Å
Rg (real space) rg_real18.37 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real1.8550e+07
I(0) uncertainty (real space) i0_real_error2.0590e+05
Rg (reciprocal space) rg_reciprocal18.39 Å
I(0) (reciprocal space) i0_reciprocal18550000.0000
Solution quality estimate total_estimate0.8053
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.0 Å
Skewness Skewness skewness0.133
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.4300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6836000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)