SAXSdb — 1bgp

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

BARLEY GRAIN PEROXIDASE

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–337	Not recorded	CA CALCIUM ION × 2 NA SODIUM ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 1.90 Å R-free 0.230

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	Q40069_HORVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–309； UniProt 29–337

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	1bgp
Deposition date deposition_date	1997-07-24
Structure title title	CRYSTAL STRUCTURE OF BARLEY GRAIN PEROXIDASE 1
Keywords keywords	PEROXIDASE, CHROMOPROTEIN, OXIDOREDUCTASE; 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	20.15 Å
Radius of gyration Rg (electron density) rg_electron	19.00 Å
Forward intensity I(0) i0	21576600.00
Molecular weight molecular_weight	34388.0 kDa
Excluded volume excluded_volume	42620 Å³
Envelope volume envelope_volume	47747 Å³
Hydration-shell volume shell_volume	20778 Å³
Envelope diameter envelope_diameter	68.1 Å
Shell Rg shell_rg	25.80 Å
Envelope Rg envelope_rg	19.44 Å
Shape Rg shape_rg	18.99 Å
Total Rg total_rg	19.93 Å
Total atoms total_atoms	2415
Residues n_residues	309
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	68.2 Å
Rg (real space) rg_real	20.09 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.1580e+07
I(0) uncertainty (real space) i0_real_error	3.0120e+05
Rg (reciprocal space) rg_reciprocal	20.10 Å
I(0) (reciprocal space) i0_reciprocal	21580000.0000
Solution quality estimate total_estimate	0.8552
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.257
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6101000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.746; Stabil: 0.980; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.936

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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	BARLEY GRAIN PEROXIDASE
Molecular weight formula_weight	33865.2 kDa
EC 编号 ec_number	1.11.1.7
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2568

AEPPVAPGLSFDFYWQTCPRAESIVREFVQEAVRKDIGLAAGLLRLHFHDCFVQGCDASVLLDGSATGPGEQQAPPNLTLRPSAFKAVNDIRDRLERECRGAVVSCSDILALAARDSVVVSGGPDYRVPLGRRDSRSFASTQDVLSDLPGPSSNVQSLLALLGRLGLDATDLVTISGGHTIGLAHCSSFEDRLFPRPDPTISPTFLSRLKRTCPAKGTDRRTVLDVRTPNVFDNKYYIDLVNREGLFVSDQDLFTNAITRPIVERFAQSQQDFFEQFGVSIGKMGQMRVRTSDQGEVRRNCSVRNPGPG

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bgpa_
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.93.1.1 — CCP-like

CATH v4.4 (2 domains)

Domain ID domain_id	1bgpA01
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	1bgpA02
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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8. Citations (1)

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Unit-cell length a length_a	71.920 Å
Unit-cell length b length_b	105.060 Å
Unit-cell length c length_c	40.950 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	38.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2300

fit	/app/data/saxs_computation/bg/1bgp/1bgp.fit
pddf	/app/data/pr_computation/bg/1bgp/1bgp.pr.out
profile	/app/data/saxs_computation/bg/1bgp/1bgp.dat

CRYSTAL STRUCTURE OF BARLEY GRAIN PEROXIDASE 1

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

BARLEY GRAIN PEROXIDASE

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