SAXSdb — 1ylb

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

Plastocyanin, chloroplast

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 70–168	Fragment：Reduced spinach plastocyanin (Residues 70-168)	CU1 COPPER (I) ION × 1	SOLUTION NMR NMR measurement conditions：pH 7.5；293 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure ambient NMR sample composition：1-2 mM wild type reduced spinach plastocyanin, 50mM sodium phosphate buffer \| 90% H2O/10% D2O	Resolution not provided

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 1YLB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AG6 PLASTOCYANIN FROM SPINACH Deposited 1997-04-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Mutation：G8D	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；pH 4.4	Resolution 1.60 Å R-free 0.224
1OOW The crystal structure of the spinach plastocyanin double mutant G8D/L12E gives insight into its low reactivity towards photosystem 1 and cytochrome f Deposited 2003-03-04	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Mutation：G8D, L12E	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；300 K；32% PEG 3350, 0.25M MgCl2, 0.1M Na-ascorbate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.00 Å R-free 0.232
1TEF Crystal structure of the spinach plastocyanin mutants G8D/K30C/T69C and K30C/T69C- a study of the effect on crystal packing and thermostability from the introduction of a novel disulfide bond Deposited 2004-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Mutation：G8D, K30C, T69C	CU COPPER (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；21% PEG 3350, 0.25M MgCl2, 0.1M Na-acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.204
1TEF Crystal structure of the spinach plastocyanin mutants G8D/K30C/T69C and K30C/T69C- a study of the effect on crystal packing and thermostability from the introduction of a novel disulfide bond Deposited 2004-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 70–168（99 aa）	Mutation：G8D, K30C, T69C	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；21% PEG 3350, 0.25M MgCl2, 0.1M Na-acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.90 Å R-free 0.204
1TEG Crystal structure of the spinach plastocyanin mutants G8D/K30C/T69C and K30C/T69C- a study of the effect on crystal packing and thermostability from the introduction of a novel disulfide bond Deposited 2004-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Mutation：K30C, T69C	CU COPPER (II) ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；21% PEG 3350, 0.25M MgCl2, 0.1M Na-acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.96 Å R-free 0.304
1TEG Crystal structure of the spinach plastocyanin mutants G8D/K30C/T69C and K30C/T69C- a study of the effect on crystal packing and thermostability from the introduction of a novel disulfide bond Deposited 2004-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 70–168（99 aa）	Mutation：K30C, T69C	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；21% PEG 3350, 0.25M MgCl2, 0.1M Na-acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.96 Å R-free 0.304
2PCF THE COMPLEX OF CYTOCHROME F AND PLASTOCYANIN DETERMINED WITH PARAMAGNETIC NMR. BASED ON THE STRUCTURES OF CYTOCHROME F AND PLASTOCYANIN, 10 STRUCTURES Deposited 1997-12-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 6；300 K	Resolution not provided
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: 17-meric	Chain Q 70–168（99 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 6 PL9 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE × 7 CLA CHLOROPHYLL A × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 BCR BETA-CAROTENE × 2 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLAS_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–99； UniProt 70–168

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	1ylb
Deposition date deposition_date	2005-01-19
Structure title title	NMR solution structure of the reduced spinach plastocyanin
Keywords keywords	plastocyanin, copper(+)-containing, electron-transfer, spinach, photosynthesis, blue-copper protein, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	13.93 Å
Radius of gyration Rg (electron density) rg_electron	12.37 Å
Forward intensity I(0) i0	2358220.00
Molecular weight molecular_weight	10467.0 kDa
Excluded volume excluded_volume	13012 Å³
Envelope volume envelope_volume	14468 Å³
Hydration-shell volume shell_volume	10066 Å³
Envelope diameter envelope_diameter	40.9 Å
Shell Rg shell_rg	18.01 Å
Envelope Rg envelope_rg	12.71 Å
Shape Rg shape_rg	12.36 Å
Total Rg total_rg	13.72 Å
Total atoms total_atoms	1435
Residues n_residues	99
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	43.5 Å
Rg (real space) rg_real	13.84 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	2.3580e+06
I(0) uncertainty (real space) i0_real_error	2.4300e+04
Rg (reciprocal space) rg_reciprocal	13.85 Å
I(0) (reciprocal space) i0_reciprocal	2358000.0000
Solution quality estimate total_estimate	0.9003
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.1 Å
Skewness Skewness skewness	0.142
Kurtosis Kurtosis kurtosis	-0.415
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	433300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ylbb_
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	1ylbB00
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	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	Plastocyanin, chloroplast
Molecular weight formula_weight	10420.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	1435

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

NMR solution structure of the reduced spinach plastocyanin

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

Plastocyanin, chloroplast

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/yl/1ylb/1ylb.fit
pddf	/app/data/pr_computation/yl/1ylb/1ylb.pr.out
profile	/app/data/saxs_computation/yl/1ylb/1ylb.dat