SAXSdb — 1r61

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

metal-dependent hydrolase

Geobacillus stearothermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 SULFATE ION × 12 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 SULFATE ION × 24 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P84132_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 1–207 Author chain B； PDBConstruct 1–207； UniProt 1–207

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	1r61
Deposition date deposition_date	2003-10-14
Structure title title	The structure of predicted metal-dependent hydrolase from Bacillus stearothermophilus
Keywords keywords	;zinc-dependent hydrolase, structural genomics, cyclase, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

1r61__assembly_1__model_1

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

Download this curve (.dat)

1r61__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r61__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.37 Å
Rg (electron density)	22.04 Å
Total Rg	22.83 Å
Atom count	3280
Residues	410
Excluded volume	58244 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r61__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1r61__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	metal-dependent hydrolase
Molecular weight formula_weight	23084.4 kDa
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	3563

AAMKVYDVTAPIYEGMPVYKNKPEKQPKRTTITNGYVTESRIDMDVHTGTHIDAPLHMVEGGATFETIPLNDLVGPCKLFDLTHVNDRITKDDIAHLDIQEGDFVLFKTKNSFEDAFHFEFIFVAEDAARYLADKQIRGVGIDALGIERAQEGHPTHKTLFSAGVIIIEGLRLKDVPEGRYFMVAAPLKLVGTDAAPARVLLFDREP

Source Source

Source organism organism	Geobacillus stearothermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	Escherichia coli

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	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1r61a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.8 — Putative cyclase
Family Family family	c.8.8.1 — Putative cyclase

Domain ID domain_id	d1r61b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.8 — Putative cyclase
Family Family family	c.8.8.1 — Putative cyclase

CATH v4.4 (2 domains)

Domain ID domain_id	1r61A00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	50 — Putative cyclase

Domain ID domain_id	1r61B00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	50 — Putative cyclase

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Unit-cell length a length_a	118.434 Å
Unit-cell length b length_b	118.434 Å
Unit-cell length c length_c	123.542 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.1776
R_work r_work	0.1756
R_free r_free	0.2152

The structure of predicted metal-dependent hydrolase from Bacillus stearothermophilus

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

metal-dependent hydrolase

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

1r61__assembly_1__model_1

1r61__assembly_1__model_1 | I(q)

1r61__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The structure of predicted metal-dependent hydrolase from Bacillus stearothermophilus

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

metal-dependent hydrolase

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

1r61__assembly_1__model_1

1r61__assembly_1__model_1 | I(q)

1r61__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)