SAXSdb — 2rd9

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

BH0186 protein

Bacillus halodurans C-125

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 2 IMIDAZOLE × 3 GLYCEROL × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 2 IMIDAZOLE × 2 GLYCEROL × 3 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	NICKEL (II) ION × 4 IMIDAZOLE × 5 GLYCEROL × 7 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KGB8_BACHD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–193； UniProt 1–174 Author chain B； PDBConstruct 20–193； UniProt 1–174 Author chain C； PDBConstruct 20–193； UniProt 1–174 Author chain D； PDBConstruct 20–193； UniProt 1–174

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	2rd9
Deposition date deposition_date	2007-09-21
Structure title title	Crystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from bacillus halodurans c-125 at 2.30 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

2rd9__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2rd9__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rd9__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.52 Å
Rg (electron density)	27.46 Å
Total Rg	28.36 Å
Atom count	6290
Residues	735
Excluded volume	111370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rd9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2rd9__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2rd9__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	BH0186 protein
Molecular weight formula_weight	22890.2 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	6934

MGSDKIHHHHHHENLYFQGMNFQMNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSMAKRYDTDVGPWKEYLGILND

Source Source

Source organism organism	Bacillus halodurans C-125
NCBI taxonomy ID ncbi_taxonomy_id	272558
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	555

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2rd9A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	450 — dinb family like domain

Domain ID domain_id	2rd9B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	450 — dinb family like domain

Domain ID domain_id	2rd9C01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	450 — dinb family like domain

Domain ID domain_id	2rd9D01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	450 — dinb family like domain

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Unit-cell length a length_a	147.330 Å
Unit-cell length b length_b	147.330 Å
Unit-cell length c length_c	147.330 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	48

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.463 Å
R factor r_factor	0.1550
R_work r_work	0.1520
R_free r_free	0.2010

Crystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from bacillus halodurans c-125 at 2.30 A resolution

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

BH0186 protein

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

2rd9__assembly_3__model_1

2rd9__assembly_3__model_1 | I(q)

2rd9__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from bacillus halodurans c-125 at 2.30 A resolution

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

BH0186 protein

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

2rd9__assembly_3__model_1

2rd9__assembly_3__model_1 | I(q)

2rd9__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)