SAXSdb — 3pcy

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

PLASTOCYANIN

Populus nigra

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 70–168	Not recorded	HG MERCURY (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å

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 3PCY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JXG The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25 Engeneered Disulfide Bridge Deposited 2001-09-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Mutation：I21C, E25C	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.205
1JXG The 1.6 A Resolution Crystal Structure of a Mutant Poplar Plastocyanin Bearing a 21-25 Engeneered Disulfide Bridge Deposited 2001-09-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 70–168（99 aa）	Mutation：I21C, E25C	CU1 COPPER (I) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.205
1PLC ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROMS RESOLUTION Deposited 1992-03-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.33 Å
1PNC ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO INDEPENDENT REFINEMENTS OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 173K Deposited 1993-09-22	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1PND ACCURACY AND PRECISION IN PROTEIN CRYSTAL STRUCTURE ANALYSIS: TWO INDEPENDENT REFINEMENTS OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 173K Deposited 1993-09-22	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1TKW The transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR Deposited 2004-06-09	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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；303 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1 NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 11 mM；Pressure 1 NMR sample composition 0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in oxidized state in 10 mM sodium phosphate pH 6.0 \| 94% H2O, 6% D2O NMR sample composition 0.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in reduced state in 10 mM sodium phosphate pH 6.0 + 1 mM sodium ascorbate \| 94% H2O, 6% D2O	Resolution not provided
2PCY THE CRYSTAL STRUCTURE OF POPLAR APOPLASTOCYANIN AT 1.8-ANGSTROMS RESOLUTION. THE GEOMETRY OF THE COPPER-BINDING SITE IS CREATED BY THE POLYPEPTIDE Deposited 1983-11-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
4DP7 The 1.08 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 4.0 Deposited 2012-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.08 Å R-free 0.142
4DP8 The 1.07 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 4.0 Deposited 2012-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU1 COPPER (I) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.07 Å R-free 0.165
4DP9 The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 6.0 Deposited 2012-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.00 Å R-free 0.144
4DPA The 1.05 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 6.0 Deposited 2012-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.05 Å R-free 0.155
4DPB The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 8.0 Deposited 2012-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.00 Å R-free 0.136
4DPC The 1.06 Angstrom crystal structure of reduced (CuI) poplar plastocyanin A at pH 8.0 Deposited 2012-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 70–168（99 aa） Fragment：UNP residues 70-168	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.06 Å R-free 0.155
4PCY CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES Deposited 1986-09-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å
5PCY CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES Deposited 1986-09-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
6PCY CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX PH VALUES Deposited 1986-09-02	Different ligand/ion	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–168（99 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLAS1_POPNI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； 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	3pcy
Deposition date deposition_date	1985-12-10
Structure title title	THE CRYSTAL STRUCTURE OF MERCURY-SUBSTITUTED POPLAR PLASTOCYANIN AT 1.9-ANGSTROMS RESOLUTION
Keywords keywords	ELECTRON TRANSPORT PROTEIN(CUPROPROTEIN); ELECTRON TRANSPORT PROTEIN(CUPROPROTEIN)
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	13.69 Å
Radius of gyration Rg (electron density) rg_electron	12.34 Å
Forward intensity I(0) i0	2524790.00
Molecular weight molecular_weight	10677.0 kDa
Excluded volume excluded_volume	13094 Å³
Envelope volume envelope_volume	14008 Å³
Hydration-shell volume shell_volume	9858 Å³
Envelope diameter envelope_diameter	40.8 Å
Shell Rg shell_rg	17.87 Å
Envelope Rg envelope_rg	12.60 Å
Shape Rg shape_rg	12.34 Å
Total Rg total_rg	13.54 Å
Total atoms total_atoms	739
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	13.61 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	2.5250e+06
I(0) uncertainty (real space) i0_real_error	2.6060e+04
Rg (reciprocal space) rg_reciprocal	13.62 Å
I(0) (reciprocal space) i0_reciprocal	2525000.0000
Solution quality estimate total_estimate	0.7280
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.409
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	247600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.999; Smooth: 0.976

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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	10493.6 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	798

IDVLLGADDGSLAFVPSEFSISPGEKIVFKNNAGFPHNIVFDEDSIPSGVDASKISMSEEDLLNAKGETFEVALSNKGEYSFYCSPHQGAGMVGKVTVN

来源 Source

来源生物 organism	Populus nigra
NCBI Class编号 ncbi_taxonomy_id	3691

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 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	59

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3pcya_
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	3pcyA00
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 (4)

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Unit-cell length a length_a	29.830 Å
Unit-cell length b length_b	46.650 Å
Unit-cell length c length_c	57.750 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	5.500 Å
R factor r_factor	0.1600
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/pc/3pcy/3pcy.fit
pddf	/app/data/pr_computation/pc/3pcy/3pcy.pr.out
profile	/app/data/saxs_computation/pc/3pcy/3pcy.dat

THE CRYSTAL STRUCTURE OF MERCURY-SUBSTITUTED POPLAR PLASTOCYANIN AT 1.9-ANGSTROMS RESOLUTION

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