SAXSdb — 3cvd

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

Plastocyanin

Phormidium laminosum

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 35–139	Not recorded	CU1 COPPER (I) ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.50 Å R-free 0.184
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 35–139	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.50 Å R-free 0.184
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 35–139	Not recorded	CU1 COPPER (I) ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.50 Å R-free 0.184

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 3CVD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BAW PLASTOCYANIN FROM PHORMIDIUM LAMINOSUM Deposited 1998-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 35–139（105 aa） Chain B 35–139（105 aa） Chain C 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 6 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.80 Å R-free 0.258
1BAW PLASTOCYANIN FROM PHORMIDIUM LAMINOSUM Deposited 1998-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 35–139（105 aa） Chain B 35–139（105 aa） Chain C 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.80 Å R-free 0.258
2Q5B High resolution structure of Plastocyanin from Phormidium laminosum Deposited 2007-05-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 1 ZN ZINC ION × 1 K POTASSIUM ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.210
2Q5B High resolution structure of Plastocyanin from Phormidium laminosum Deposited 2007-05-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 1 ZN ZINC ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.210
2Q5B High resolution structure of Plastocyanin from Phormidium laminosum Deposited 2007-05-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 1 ZN ZINC ION × 2 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.210
2Q5B High resolution structure of Plastocyanin from Phormidium laminosum Deposited 2007-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 35–139（105 aa） Chain B 35–139（105 aa） Chain C 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 4 K POTASSIUM ION × 5 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.210
2Q5B High resolution structure of Plastocyanin from Phormidium laminosum Deposited 2007-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 35–139（105 aa） Chain B 35–139（105 aa） Chain C 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 4 K POTASSIUM ION × 5 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.210
2W88 Plastocyanin variant with N-terminal Methionine - open structure Deposited 2009-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 35–139（105 aa） Chain B 35–139（105 aa） Chain C 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 6 ZN ZINC ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M ZINC ACETATE, 0.4 M SODIUM ACETATE	Resolution 2.89 Å R-free 0.223
2W8C Plastocyanin variant with N-terminal Methionine - closed structure Deposited 2009-01-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions 5% PEG 8K, 0.1M ZINC ACETATE, 0.2 M SODIUM ACETATE	Resolution 1.80 Å R-free 0.224
2W8C Plastocyanin variant with N-terminal Methionine - closed structure Deposited 2009-01-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions 5% PEG 8K, 0.1M ZINC ACETATE, 0.2 M SODIUM ACETATE	Resolution 1.80 Å R-free 0.224
2W8C Plastocyanin variant with N-terminal Methionine - closed structure Deposited 2009-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 35–139（105 aa） Chain B 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 6 ZN ZINC ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions 5% PEG 8K, 0.1M ZINC ACETATE, 0.2 M SODIUM ACETATE	Resolution 1.80 Å R-free 0.224
3BQV Crystal Structure of the double mutant D44A D45A Plastocyanin from Phormidium laminosum Deposited 2007-12-20	Different construct 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 35–139（105 aa） Fragment：UNP residues 35-139	Mutation：D44A, D45A	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% PEG 8000, 0.1 M Sodium cacodylate, 0.2 M Sodium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.50 Å R-free 0.245
3CVB Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization Deposited 2008-04-18	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–139（105 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å R-free 0.183
3CVB Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization Deposited 2008-04-18	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 35–139（105 aa）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å R-free 0.183
3CVC Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization Deposited 2008-04-18	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–139（105 aa）	Not recorded	CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.72 Å R-free 0.192
4R0O Crystal structure of PEGylated plastocyanin at 4.2 A resolution Deposited 2014-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–139（105 aa） Fragment：UNP residues 35-139	Not recorded	CU COPPER (II) ION × 1 LCY 1-methylpyrrolidine-2,5-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293.15 K；48 % AMMONIUM SULPHATE, 30 mM POTASSIUM FERRICYANIDE, 100 mM SODIUM ACETATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 4.20 Å R-free 0.270
4R0O Crystal structure of PEGylated plastocyanin at 4.2 A resolution Deposited 2014-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 35–139（105 aa） Fragment：UNP residues 35-139	Not recorded	CU COPPER (II) ION × 1 LCY 1-methylpyrrolidine-2,5-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293.15 K；48 % AMMONIUM SULPHATE, 30 mM POTASSIUM FERRICYANIDE, 100 mM SODIUM ACETATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 4.20 Å R-free 0.270
4R0O Crystal structure of PEGylated plastocyanin at 4.2 A resolution Deposited 2014-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 35–139（105 aa） Fragment：UNP residues 35-139	Not recorded	CU COPPER (II) ION × 1 LCY 1-methylpyrrolidine-2,5-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293.15 K；48 % AMMONIUM SULPHATE, 30 mM POTASSIUM FERRICYANIDE, 100 mM SODIUM ACETATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 4.20 Å R-free 0.270
4R0O Crystal structure of PEGylated plastocyanin at 4.2 A resolution Deposited 2014-08-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 35–139（105 aa） Fragment：UNP residues 35-139	Not recorded	CU COPPER (II) ION × 1 LCY 1-methylpyrrolidine-2,5-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293.15 K；48 % AMMONIUM SULPHATE, 30 mM POTASSIUM FERRICYANIDE, 100 mM SODIUM ACETATE, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 4.20 Å R-free 0.270

8 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLAS_PHOLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–105； UniProt 35–139 Author chain B； PDBConstruct 1–105； UniProt 35–139 Author chain C； PDBConstruct 1–105； UniProt 35–139

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	3cvd
Deposition date deposition_date	2008-04-18
Structure title title	Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization
Keywords keywords	Cupredoxin, Self Assemby, Copper, Electron transport, Metal-binding, 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	21.93 Å
Radius of gyration Rg (electron density) rg_electron	21.10 Å
Forward intensity I(0) i0	20016300.00
Molecular weight molecular_weight	33931.0 kDa
Excluded volume excluded_volume	42228 Å³
Envelope volume envelope_volume	50183 Å³
Hydration-shell volume shell_volume	20185 Å³
Envelope diameter envelope_diameter	66.3 Å
Shell Rg shell_rg	26.87 Å
Envelope Rg envelope_rg	20.90 Å
Shape Rg shape_rg	21.08 Å
Total Rg total_rg	21.91 Å
Total atoms total_atoms	2372
Residues n_residues	312
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	65.3 Å
Rg (real space) rg_real	21.79 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.0020e+07
I(0) uncertainty (real space) i0_real_error	2.6030e+05
Rg (reciprocal space) rg_reciprocal	21.82 Å
I(0) (reciprocal space) i0_reciprocal	20020000.0000
Solution quality estimate total_estimate	0.9195
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.076
Kurtosis Kurtosis kurtosis	-0.653
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1770000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.984; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Plastocyanin
Molecular weight formula_weight	11465.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2960

ETFTVKMGADSGLFQFEPANVTVHPGDTVKWVNNKLPPHNILFDDKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG

来源 Source

来源生物 organism	Phormidium laminosum
NCBI Class编号 ncbi_taxonomy_id	32059
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	479

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3cvda_
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	d3cvdb_
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	d3cvdc_
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 (3 domains)

Domain ID domain_id	3cvdA00
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	3cvdB00
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	3cvdC00
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	85.843 Å
Unit-cell length b length_b	85.843 Å
Unit-cell length c length_c	90.282 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	28.770 Å
R factor r_factor	0.1550
R_work r_work	0.1530
R_free r_free	0.1840

fit	/app/data/saxs_computation/cv/3cvd/3cvd.fit
pddf	/app/data/pr_computation/cv/3cvd/3cvd.pr.out
profile	/app/data/saxs_computation/cv/3cvd/3cvd.dat

Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization