SAXSdb — 4kqn

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

D-hydantoinase

Bacillus sp. AR9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5DLU2_9BACI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–459； UniProt 2–460 Author chain B； PDBConstruct 1–459； UniProt 2–460

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	4kqn
Deposition date deposition_date	2013-05-15
Structure title title	2.8 Angstrom Resolution Crystal Structure of D-Hydantoinase from Bacillus sp. AR9 in C2221 Space Group
Keywords keywords	TIM-barrel, hydantoinase, binuclear metal-binding, 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.

4kqn__assembly_1__model_1

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

Download this curve (.dat)

4kqn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4kqn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.13 Å
Rg (electron density)	32.89 Å
Total Rg	33.21 Å
Atom count	7055
Residues	916
Excluded volume	125300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4kqn__assembly_1__model_1`	dimeric （2）	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	50224.6 kDa
EC 编号 ec_number	3.5.2.2
Mutation mutation	S36A, V37A, N38A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7085

KKWIRGGTVVTAADTYQADVLIEGERVVAIGHQLAAAGAEEIDATGCYVIPGGIDPHTHLDMPFGGTVTADDFFTGTRAAAFGGTTSIVDFCLTKKGESLKSAIATWHEKARGKAVIDYGFHLMIAEANDQVLEELESVISSEGITSLKVFMAYKNVFQADDETLFKTLVKAKELGALVQVHAENGDVLDYLTKKALAEGNTDPIYHAYTRPPEAEGEATGRAIALTALAGSQLYVVHVSCASAVQRIAEAREKGWNVYGETCPQYLALDVSIMDQPDFEGAKYVWSPPLREKWNQEVLWSALKNGILQTVGSDHCPFNFRGQKELGRGDFTKIPNGGPLIEDRLTILYSEGVRQGRISLNQFVDISSTKAAKLFGMFPRKGTIAVGSDADIVIFDPHVKRTLSVETHHMNVDYNPFEGMEVYGEVVSVLSRGSFVVRDKQFVGQAGSGQYIKRTTFEQA

Source Source

Source organism organism	Bacillus sp. AR9
NCBI taxonomy ID ncbi_taxonomy_id	301298
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4kqnA01
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	4kqnA02
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	4kqnB01
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	4kqnB02
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	90.877 Å
Unit-cell length b length_b	185.239 Å
Unit-cell length c length_c	113.447 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	25.410 Å
R factor r_factor	0.2092
R_work r_work	0.2061
R_free r_free	0.2666

2.8 Angstrom Resolution Crystal Structure of D-Hydantoinase from Bacillus sp. AR9 in C2221 Space Group

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

4kqn__assembly_1__model_1

4kqn__assembly_1__model_1 | I(q)

4kqn__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

2.8 Angstrom Resolution Crystal Structure of D-Hydantoinase from Bacillus sp. AR9 in C2221 Space Group

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

4kqn__assembly_1__model_1

4kqn__assembly_1__model_1 | I(q)

4kqn__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)