SAXSdb — 3gyg

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

NTD biosynthesis operon putative hydrolase ntdB

Bacillus subtilis subsp. subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 water × 4	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NTDB_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–289； UniProt 1–286 Author chain B； PDBConstruct 4–289； UniProt 1–286 Author chain C； PDBConstruct 4–289； UniProt 1–286 Author chain D； PDBConstruct 4–289； UniProt 1–286

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	3gyg
Deposition date deposition_date	2009-04-03
Structure title title	Crystal structure of yhjK (haloacid dehalogenase-like hydrolase protein) from Bacillus subtilis
Keywords keywords	;PF05116, PF08282, MCSG, PSI-2, haloacid dehalogenase-like hydrolase, Structural Genomics, Protein Structure Initiative, Midwest Center for Structural Genomics, Antibiotic biosynthesis, 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.

3gyg__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gyg__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gyg__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	21.82 Å
Rg (electron density)	20.88 Å
Total Rg	21.64 Å
Atom count	2207
Residues	273
Excluded volume	38969 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gyg__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gyg__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gyg__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3gyg__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3gyg__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Description description	NTD biosynthesis operon putative hydrolase ntdB
Molecular weight formula_weight	33750.0 kDa
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	8445

SNAMLLSKKSEYKTLSTVEHPQYIVFCDFDETYFPHTIDEQKQQDIYELEDYLEQKSKDGELIIGWVTGSSIESILDKMGRGKFRYFPHFIASDLGTEITYFSEHNFGQQDNKWNSRINEGFSKEKVEKLVKQLHENHNILLNPQTQLGKSRYKHNFYYQEQDEINDKKNLLAIEKICEEYGVSVNINRCNPLAGDPEDSYDVDFIPIGTGKNEIVTFMLEKYNLNTERAIAFGDSGNDVRMLQTVGNGYLLKNATQEAKNLHNLITDSEYSKGITNTLKKLIGFMRRK

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	81

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6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	3gygA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3gygA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1410 — yhjk (haloacid dehalogenase-like hydrolase protein) domain

Domain ID domain_id	3gygB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3gygC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3gygC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1410 — yhjk (haloacid dehalogenase-like hydrolase protein) domain

Domain ID domain_id	3gygD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	3gygD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1410 — yhjk (haloacid dehalogenase-like hydrolase protein) domain

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Unit-cell length a length_a	72.077 Å
Unit-cell length b length_b	111.732 Å
Unit-cell length c length_c	135.173 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2140
R_work r_work	0.2100
R_free r_free	0.2770

Crystal structure of yhjK (haloacid dehalogenase-like hydrolase protein) from Bacillus subtilis

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

NTD biosynthesis operon putative hydrolase ntdB

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

3gyg__assembly_4__model_1

3gyg__assembly_4__model_1 | I(q)

3gyg__assembly_4__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) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)

Crystal structure of yhjK (haloacid dehalogenase-like hydrolase protein) from Bacillus subtilis

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

NTD biosynthesis operon putative hydrolase ntdB

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

3gyg__assembly_4__model_1

3gyg__assembly_4__model_1 | I(q)

3gyg__assembly_4__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) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)