SAXSdb — 1a4e

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

CATALASE A

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 15–502 Chain B； UniProt 15–502 Chain C； UniProt 15–502 Chain D； UniProt 15–502	Not recorded	AZI AZIDE ION × 4 SO4 SULFATE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 2.40 Å R-free 0.198

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CATA_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–488； UniProt 15–502 Author chain B； PDBConstruct 1–488； UniProt 15–502 Author chain C； PDBConstruct 1–488； UniProt 15–502 Author chain D； PDBConstruct 1–488； UniProt 15–502

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	1a4e
Deposition date deposition_date	1998-01-29
Structure title title	CATALASE A FROM SACCHAROMYCES CEREVISIAE
Keywords keywords	OXIDOREDUCTASE, CATALASE, PEROXIDASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.26 Å
Radius of gyration Rg (electron density) rg_electron	35.61 Å
Forward intensity I(0) i0	781073000.00
Molecular weight molecular_weight	225060.0 kDa
Excluded volume excluded_volume	279440 Å³
Envelope volume envelope_volume	329060 Å³
Hydration-shell volume shell_volume	71439 Å³
Envelope diameter envelope_diameter	114.6 Å
Shell Rg shell_rg	45.73 Å
Envelope Rg envelope_rg	35.74 Å
Shape Rg shape_rg	35.58 Å
Total Rg total_rg	36.28 Å
Total atoms total_atoms	15922
Residues n_residues	1952
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	110.7 Å
Rg (real space) rg_real	36.03 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	7.8110e+08
I(0) uncertainty (real space) i0_real_error	1.1150e+07
Rg (reciprocal space) rg_reciprocal	36.18 Å
I(0) (reciprocal space) i0_reciprocal	781200000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.3 Å
Skewness Skewness skewness	0.138
Kurtosis Kurtosis kurtosis	-0.518
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	308600000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.916

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	CATALASE A
Molecular weight formula_weight	55623.9 kDa
EC 编号 ec_number	1.11.1.6
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16879

DVREDRVVTNSTGNPINEPFVTQRIGEHGPLLLQDYNLIDSLAHFNRENIPQRNPHAHGSGAFGYFEVTDDITDICGSAMFSKIGKRTKCLTRFSTVGGDKGSADTVRDPRGFATKFYTEEGNLDWVYNNTPVFFIRDPSKFPHFIHTQKRNPQTNLRDADMFWDFLTTPENQVAIHQVMILFSDRGTPANYRSMHGYSGHTYKWSNKNGDWHYVQVHIKTDQGIKNLTIEEATKIAGSNPDYCQQDLFEAIQNGNYPSWTVYIQTMTERDAKKLPFSVFDLTKVWPQGQFPLRRVGKIVLNENPLNFFAQVEQAAFAPSTTVPYQEASADPVLQARLFSYADAHRYRLGPNFHQIPVNCPYASKFFNPAIRDGPMNVNGNFGSEPTYLANDKSYTYIQQDRPIQQHQEVWNGPAIPYHWATSPGDVDFVQARNLYRVLGKQPGQQKNLAYNIGIHVEGACPQIQQRVYDMFARVDKGLSEAIKKVAE

Entity 2 Entity 2 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	957

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1a4ea_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d1a4eb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d1a4ec_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

Domain ID domain_id	d1a4ed_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.5 — Heme-dependent catalase-like
Superfamily Superfamily superfamily	e.5.1 — Heme-dependent catalase-like
Family Family family	e.5.1.1 — Heme-dependent catalases

CATH v4.4 (4 domains)

Domain ID domain_id	1a4eA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	1a4eB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	1a4eC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

Domain ID domain_id	1a4eD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	180 — Catalase HpII, Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Catalase core domain

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8. Citations (1)

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Unit-cell length a length_a	184.172 Å
Unit-cell length b length_b	184.172 Å
Unit-cell length c length_c	304.977 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1540
R_work r_work	0.1540
R_free r_free	0.1980

fit	/app/data/saxs_computation/a4/1a4e/1a4e.fit
pddf	/app/data/pr_computation/a4/1a4e/1a4e.pr.out
profile	/app/data/saxs_computation/a4/1a4e/1a4e.dat

CATALASE A FROM SACCHAROMYCES CEREVISIAE

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

CATALASE A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction