1nfg

Structure of D-hydantoinase

Method: X-RAY DIFFRACTION

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

D-hydantoinase

Ralstonia pickettii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HYDA_BURPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–457； UniProt 1–457 Author chain B； PDBConstruct 1–457； UniProt 1–457 Author chain C； PDBConstruct 1–457； UniProt 1–457 Author chain D； PDBConstruct 1–457； UniProt 1–457

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	1nfg
Deposition date deposition_date	2002-12-14
Structure title title	Structure of D-hydantoinase
Keywords keywords	TIM barrel, HYDROLASE; HYDROLASE
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.

1nfg__assembly_1__model_1

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

Download this curve (.dat)

1nfg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nfg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.38 Å
Rg (electron density)	36.69 Å
Total Rg	37.17 Å
Atom count	14060
Residues	1824
Excluded volume	250130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nfg__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	D-hydantoinase
Molecular weight formula_weight	50039.8 kDa
EC 编号 ec_number	3.5.2.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14564

MDIIIKNGTIVTADGISRADLGIKDGKITQIGGALGPAERTIDAAGRYVFPGGIDVHTHVETVSFNTQSADTFATATVAAACGGTTTIVDFCQQDRGHSLAEAVAKWDGMAGGKSAIDYGYHIIVLDPTDSVIEELEVLPDLGITSFKVFMAYRGMNMIDDVTLLKTLDKAVKTGSLVMVHAENGDAADYLRDKFVAEGKTAPIYHALSRPPRVEAEATARALALAEIVNAPIYIVHVTCEESLEEVMRAKSRGVRALAETCTHYLYLTKEDLERPDFEGAKYVFTPPARAKKDHDVLWNALRNGVFETVSSDHCSWLFKGHKDRGRNDFRAIPNGAPGVEERLMMVYQGVNEGRISLTQFVELVATRPAKVFGMFPQKGTIAVGSDADIVLWDPEAEMVIEQTAMHNAMDYSSYEGHKVKGVPKTVLLRGKVIVDEGSYVGEPTDGKFLKRRKYKQ

Source Source

Source organism organism	Ralstonia pickettii
NCBI taxonomy ID ncbi_taxonomy_id	329
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	504

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1nfga1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d1nfga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

Domain ID domain_id	d1nfgb1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d1nfgb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

Domain ID domain_id	d1nfgc1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d1nfgc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

Domain ID domain_id	d1nfgd1
Class class	b — All beta proteins
Fold Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
Family Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

Domain ID domain_id	d1nfgd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
Family Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

CATH v4.4 (8 domains)

Domain ID domain_id	1nfgA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1nfgA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	1nfgB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1nfgB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	1nfgC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1nfgC02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	1nfgD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily	10 — Urease, subunit C, domain 1

Domain ID domain_id	1nfgD02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	68.700 Å
Unit-cell length b length_b	170.500 Å
Unit-cell length c length_c	87.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	14.940 Å
R factor r_factor	0.2210
R_work r_work	0.2200
R_free r_free	0.2390

Structure of D-hydantoinase

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

D-hydantoinase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1nfg__assembly_1__model_1

1nfg__assembly_1__model_1 | I(q)

1nfg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of D-hydantoinase

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

D-hydantoinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1nfg__assembly_1__model_1

1nfg__assembly_1__model_1 | I(q)

1nfg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)