SAXSdb — 1ub2

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

Catalase-peroxidase

Synechococcus elongatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PROTOPORPHYRIN IX CONTAINING FE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q55110_SYNSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–720； UniProt 1–720

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	1ub2
Deposition date deposition_date	2003-03-28
Structure title title	Crystal structure of catalase-peroxidase from Synechococcus PCC 7942
Keywords keywords	catalase-peroxidase, catalase, peroxidase, KatG, Synechococcus PCC 7942, Cyanobacteria, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

1ub2__assembly_1__model_1

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

Download this curve (.dat)

1ub2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ub2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.37 Å
Rg (electron density)	34.65 Å
Total Rg	35.17 Å
Atom count	11080
Residues	1400
Excluded volume	194940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ub2__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	Catalase-peroxidase
Molecular weight formula_weight	79999.6 kDa
EC 编号 ec_number	1.11.1.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6243

MTATQGKCPVMHGGATTVNISTAEWWPKALNLDILSQHDRKTNPMGPDFNYQEEVQKLDAALKQDLQALMTDSQDWWPADWGHYGGLMIRLTWHAAGTYRIADGRGGAGTGNQRFAPLNSWPDNTNLDKARRLLWPIKQKYGNKLSWADLIAYAGTIAYESMGLKTFGFAFGREDIWHPEKDIYWGPEKEWFPPSTNPNSRYTGDRELENPLAAVTMGLIYVNPEGVDGNPDPLKTAHDVRVTFARMAMNDEETVALTAGGHTVGKCHGNGNAALLGPEPEGADVEDQGLGWINKTQSGIGRNAVTSGLEGAWTPHPTQWDNGYFAVCSLNYDWELKKNPAGAWQWEPINPREEDLPVDVEDPSIRRNLVMTDADMAMKMDPEYRKISERFYQDPAYFADVFARAWFKLTHRDMGPKARYIGPDVPQEDLIWQDPIPAGNRNYDVQAVKDRIAASGLSISELVSTAWDSARTYRNSDKRGGANGARIRLAPQKDWEGNEPDRLPKVLAVLEGISAATGATVADVIVLAGNVGVEQKARAAGVEIVLPFAPGRGDATAEQTDTESFAVLEPIHDAIATGSSRTMRQRLKNCCLIATQLLGLTAPEMTVLIGGLRVLGTNHGGTKHVVFTDREGVLTNDFFVNLTDMNYLWKPAGKNLYEICDRKTNQVKWTATRVDLVFGSNSILRAYSELYAQDDNKEKFVRDFVAAWTKVMNADRFDLD

Source Source

Source organism organism	Synechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	1140
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	703

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ub2a1
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.3 — Catalase-peroxidase KatG

Domain ID domain_id	d1ub2a2
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.3 — Catalase-peroxidase KatG

CATH v4.4 (4 domains)

Domain ID domain_id	1ub2A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ub2A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

Domain ID domain_id	1ub2A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ub2A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

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Unit-cell length a length_a	109.208 Å
Unit-cell length b length_b	109.208 Å
Unit-cell length c length_c	202.661 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	14.980 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2320

Crystal structure of catalase-peroxidase from Synechococcus PCC 7942

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

Catalase-peroxidase

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

1ub2__assembly_1__model_1

1ub2__assembly_1__model_1 | I(q)

1ub2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of catalase-peroxidase from Synechococcus PCC 7942

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

Catalase-peroxidase

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

1ub2__assembly_1__model_1

1ub2__assembly_1__model_1 | I(q)

1ub2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)