SAXSdb — 4r0o

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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	Fragment：UNP residues 35-139	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 35–139	Fragment：UNP residues 35-139	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 35–139	Fragment：UNP residues 35-139	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 35–139	Fragment：UNP residues 35-139	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

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 4R0O	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 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）	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 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）	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 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）	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 construct 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 construct 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 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 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）	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 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）	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 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）	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
3CVD Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization Deposited 2008-04-18	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）	Not recorded	CU1 COPPER (I) ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.184
3CVD Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization Deposited 2008-04-18	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）	Not recorded	CU1 COPPER (I) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.184
3CVD Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization Deposited 2008-04-18	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）	Not recorded	CU1 COPPER (I) ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.184

8 other PDB entries and 18 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 2–106； UniProt 35–139 Author chain B； PDBConstruct 2–106； UniProt 35–139 Author chain C； PDBConstruct 2–106； UniProt 35–139 Author chain D； PDBConstruct 2–106； 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	4r0o
Deposition date deposition_date	2014-08-01
Structure title title	Crystal structure of PEGylated plastocyanin at 4.2 A resolution
Keywords keywords	PEGylation, 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	23.82 Å
Radius of gyration Rg (electron density) rg_electron	22.92 Å
Forward intensity I(0) i0	37550400.00
Molecular weight molecular_weight	46851.0 kDa
Excluded volume excluded_volume	58336 Å³
Envelope volume envelope_volume	70608 Å³
Hydration-shell volume shell_volume	25794 Å³
Envelope diameter envelope_diameter	78.4 Å
Shell Rg shell_rg	29.81 Å
Envelope Rg envelope_rg	22.95 Å
Shape Rg shape_rg	22.90 Å
Total Rg total_rg	23.83 Å
Total atoms total_atoms	3280
Residues n_residues	424
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	76.8 Å
Rg (real space) rg_real	23.73 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.7550e+07
I(0) uncertainty (real space) i0_real_error	5.2170e+05
Rg (reciprocal space) rg_reciprocal	23.76 Å
I(0) (reciprocal space) i0_reciprocal	37550000.0000
Solution quality estimate total_estimate	0.8209
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4271000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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	Plastocyanin
Molecular weight formula_weight	11551.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3280

METFTVKMGADSGLLQFEPANVTVHPGDTVKWVNNKLPPHNILFDCKQVPGASKELADKLSHSQLMFSPGESYEITFSSDFPAGTYTYYCAPHRGAGMVGKITVEG

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 (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1-methylpyrrolidine-2,5-dione
Molecular weight formula_weight	113.1 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	116.140 Å
Unit-cell length b length_b	116.140 Å
Unit-cell length c length_c	172.140 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	43.035 Å
R factor r_factor	0.2304
R_work r_work	0.2285
R_free r_free	0.2699

fit	/app/data/saxs_computation/r0/4r0o/4r0o.fit
pddf	/app/data/pr_computation/r0/4r0o/4r0o.pr.out
profile	/app/data/saxs_computation/r0/4r0o/4r0o.dat

Crystal structure of PEGylated plastocyanin at 4.2 A 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

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