SAXSdb — 1y1f

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Other combination	Monomer	1 / 0 / 0 / 1	Consistent with protein count

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	1y1f
Deposition date deposition_date	2004-11-18
Structure title title	human formylglycine generating enzyme with cysteine sulfenic acid
Keywords keywords	Formylglycine, multiple sulfatase deficiency, cysteine sulfenic acid, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1y1f__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1y1f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y1f__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.47 Å
Rg (electron density)	17.55 Å
Total Rg	18.54 Å
Atom count	2192
Residues	271
Excluded volume	38331 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y1f__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	C-alpha-formyglycine-generating enzyme
Molecular weight formula_weight	34924.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	2658

EANAPGPVPGERQLAHSKMVPIPAGVFTMGTDDPQIKQDGEAPARRVTIDAFYMDAYEVSNTEFEKFVNSTGYLTEAEKFGDSFVFEGMLSEQVKTNIQQAVAAAPWWLPVKGANWRHPEGPDSTILHRPDHPVLHVSWNDAVAYCTWAGKRLPTEAEWEYSCRGGLHNRLFPWGNKLQPKGQHYANIWQGEFPVTNTGEDGFQGTAPVDAFPPNGYGLYNIVGNAWEWTSDWWTVHHSVEETLNPKGPPSGKDRVKKGGSYMCHRSYCYRYRCAARSQNTPDSSASNLGFRCAADRLPTMDRGSHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	429

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1y1fx_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.7 — Sulfatase-modifying factor-like

CATH v4.4 (1 domains)

Domain ID domain_id	1y1fX00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1580 — paralog of FGE (formylglycine-generating enzyme)
Homologous superfamily homologous superfamily	10 — paralog of FGE (formylglycine-generating enzyme)

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Unit-cell length a length_a	61.754 Å
Unit-cell length b length_b	109.692 Å
Unit-cell length c length_c	43.411 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	29.750 Å
R factor r_factor	0.1502
R_work r_work	0.1481
R_free r_free	0.1936

human formylglycine generating enzyme with cysteine sulfenic acid