SAXSdb — 1bxu

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

PLASTOCYANIN

Synechococcus elongatus

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 35–125	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.3；pH 5.3	Resolution 1.90 Å R-free 0.187

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 1BXU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BXV REDUCED PLASTOCYANIN FROM SYNECHOCOCCUS SP. Deposited 1998-10-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–125（91 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 1.80 Å R-free 0.195

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

View Construct and Data Evidence

UniProt name	PLAS_SYNP7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–91； UniProt 35–125

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	1bxu
Deposition date deposition_date	1998-10-09
Structure title title	OXIDIZED PLASTOCYANIN FROM SYNECHOCOCCUS SP.
Keywords keywords	COPPER PROTEIN, ELECTRON TRANSFER; COPPER PROTEIN
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	13.28 Å
Radius of gyration Rg (electron density) rg_electron	12.01 Å
Forward intensity I(0) i0	2146440.00
Molecular weight molecular_weight	9911.0 kDa
Excluded volume excluded_volume	12277 Å³
Envelope volume envelope_volume	13115 Å³
Hydration-shell volume shell_volume	9515 Å³
Envelope diameter envelope_diameter	39.4 Å
Shell Rg shell_rg	17.39 Å
Envelope Rg envelope_rg	12.22 Å
Shape Rg shape_rg	11.99 Å
Total Rg total_rg	13.30 Å
Total atoms total_atoms	694
Residues n_residues	91
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	43.9 Å
Rg (real space) rg_real	13.19 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	2.1460e+06
I(0) uncertainty (real space) i0_real_error	2.3680e+04
Rg (reciprocal space) rg_reciprocal	13.19 Å
I(0) (reciprocal space) i0_reciprocal	2146000.0000
Solution quality estimate total_estimate	0.8857
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.1 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.438
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	378100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998

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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	PLASTOCYANIN
Molecular weight formula_weight	9861.0 kDa
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	776

QTVAIKMGADNGMLAFEPSTIEIQAGDTVQWVNNKLAPHNVVVEGQPELSHKDLAFSPGETFEATFSEPGTYTYYCEPHRGAGMVGKIVVQ

来源 Source

来源生物 organism	Synechococcus elongatus
NCBI Class编号 ncbi_taxonomy_id	1140
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	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	82

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bxua_
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 (1 domains)

Domain ID domain_id	1bxuA00
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 (2)

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Unit-cell length a length_a	43.100 Å
Unit-cell length b length_b	43.100 Å
Unit-cell length c length_c	56.900 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 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1510
R_work r_work	0.1670
R_free r_free	0.1870

fit	/app/data/saxs_computation/bx/1bxu/1bxu.fit
pddf	/app/data/pr_computation/bx/1bxu/1bxu.pr.out
profile	/app/data/saxs_computation/bx/1bxu/1bxu.dat

OXIDIZED PLASTOCYANIN FROM SYNECHOCOCCUS SP.

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

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