SAXSdb — 1byo

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

PROTEIN (PLASTOCYANIN)

Silene latifolia subsp. alba

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 67–165	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；53% SATURATED AMMONIUM SULFATE, 0.1 M SODIUM ACETATE BUFFER, pH 5.5	Resolution 2.00 Å R-free 0.225
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 67–165	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；53% SATURATED AMMONIUM SULFATE, 0.1 M SODIUM ACETATE BUFFER, pH 5.5	Resolution 2.00 Å R-free 0.225

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.

Other PDB	Difference from Current Entry 1BYO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BYP E43K,D44K DOUBLE MUTANT PLASTOCYANIN FROM SILENE Deposited 1998-10-19	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 67–165（99 aa）	Mutation：E43K, D44K	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；2.8M AMMONIUM SULFATE, 100MM POTASSIUM PHOSPHATE, pH 7.0	Resolution 1.75 Å R-free 0.199

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLAS_SILPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 67–165 Author chain B； PDBConstruct 1–99； UniProt 67–165

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	1byo
Deposition date deposition_date	1998-10-19
Structure title title	WILD-TYPE PLASTOCYANIN FROM SILENE
Keywords keywords	ELECTRON TRANSFER, PHOTOSYNTHESIS, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	20.47 Å
Radius of gyration Rg (electron density) rg_electron	19.91 Å
Forward intensity I(0) i0	8145980.00
Molecular weight molecular_weight	20894.0 kDa
Excluded volume excluded_volume	25935 Å³
Envelope volume envelope_volume	30782 Å³
Hydration-shell volume shell_volume	14009 Å³
Envelope diameter envelope_diameter	66.2 Å
Shell Rg shell_rg	24.23 Å
Envelope Rg envelope_rg	19.82 Å
Shape Rg shape_rg	19.90 Å
Total Rg total_rg	20.58 Å
Total atoms total_atoms	1464
Residues n_residues	198
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	77.9 Å
Rg (real space) rg_real	20.57 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	8.1460e+06
I(0) uncertainty (real space) i0_real_error	1.2630e+05
Rg (reciprocal space) rg_reciprocal	20.55 Å
I(0) (reciprocal space) i0_reciprocal	8146000.0000
Solution quality estimate total_estimate	0.6978
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.392
Kurtosis Kurtosis kurtosis	-0.565
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1903000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.524; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.506; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PLASTOCYANIN)
Molecular weight formula_weight	10401.5 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	1542

AEVLLGSSDGGLAFVPSDLSIASGEKITFKNNAGFPHNDLFDEDEVPAGVDVTKISMPEEDLLNAPGEEYSVTLTEKGTYKFYCAPHAGAGMVGKVTVN

来源 Source

来源生物 organism	Silene latifolia subsp. alba
NCBI Class编号 ncbi_taxonomy_id	52853
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1byoa_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d1byob_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (2 domains)

Domain ID domain_id	1byoA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	1byoB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (3)

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Unit-cell length a length_a	76.600 Å
Unit-cell length b length_b	76.600 Å
Unit-cell length c length_c	65.500 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1890
R_work r_work	0.1970
R_free r_free	0.2250

fit	/app/data/saxs_computation/by/1byo/1byo.fit
pddf	/app/data/pr_computation/by/1byo/1byo.pr.out
profile	/app/data/saxs_computation/by/1byo/1byo.dat

WILD-TYPE PLASTOCYANIN FROM SILENE

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

PROTEIN (PLASTOCYANIN)

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