SAXSdb — 3hys

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

protein Rv0554, putative Bromoperoxidase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MALONIC ACID × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 1,2-ETHANEDIOL × 7 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O06420_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 33–293； UniProt 2–262 Author chain B； PDBConstruct 33–293； UniProt 2–262

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	3hys
Deposition date deposition_date	2009-06-23
Structure title title	Structure of Rv0554 from Mycobacterium tuberculosis complexed with Malonic Acid
Keywords keywords	hydrolase, Oxidoreductase, Peroxidase; 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.

3hys__assembly_1__model_1

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

Download this curve (.dat)

3hys__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hys__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.68 Å
Rg (electron density)	26.15 Å
Total Rg	26.92 Å
Atom count	4152
Residues	536
Excluded volume	73874 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hys__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 (6)

Entity 1 Entity 1 polymer

Description description	protein Rv0554, putative Bromoperoxidase
Molecular weight formula_weight	32254.5 kDa
EC 编号 ec_number	1.11.1.-
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	4556

MSYYHHHHHHDYDIPTTENLYFQGAMDPEFRVINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MALONIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	388

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3hysa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

Domain ID domain_id	d3hysa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3hysb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3hysA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3hysB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	100.435 Å
Unit-cell length b length_b	100.435 Å
Unit-cell length c length_c	135.064 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	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1690
R_work r_work	0.1660
R_free r_free	0.2230

Structure of Rv0554 from Mycobacterium tuberculosis complexed with Malonic Acid

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

protein Rv0554, putative Bromoperoxidase

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

3hys__assembly_1__model_1

3hys__assembly_1__model_1 | I(q)

3hys__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Rv0554 from Mycobacterium tuberculosis complexed with Malonic Acid

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

protein Rv0554, putative Bromoperoxidase

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

3hys__assembly_1__model_1

3hys__assembly_1__model_1 | I(q)

3hys__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)