SAXSdb — 2pcf

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

PLASTOCYANIN

Spinacia oleracea

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 70–168	Not recorded	CYTOCHROME F × 1 （P36438） CU COPPER (II) ION × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions：pH 6；300 K	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 2PCF	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
1YLB NMR solution structure of the reduced spinach plastocyanin Deposited 2005-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 70–168（99 aa） Fragment：Reduced spinach plastocyanin (Residues 70-168)	Not recorded	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
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01	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 A； PDBConstruct 1–99； UniProt 70–168

CYTOCHROME F

Brassica rapa

UniProt P36438

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 36–285	Fragment：SOLUBLE DOMAIN	PLASTOCYANIN × 1 （P00289） CU COPPER (II) ION × 1 HEC HEME C × 1	SOLUTION NMR NMR measurement conditions：pH 6；300 K	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 2PCF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CTM CRYSTAL STRUCTURE OF CHLOROPLAST CYTOCHROME F REVEALS A NOVEL CYTOCHROME FOLD AND UNEXPECTED HEME LIGATION Deposited 1994-01-02	Different construct Different oligomeric state 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 36–285（250 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.277
1HCZ LUMEN-SIDE DOMAIN OF REDUCED CYTOCHROME F AT-35 DEGREES CELSIUS Deposited 1996-09-18	Different construct Different oligomeric state 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 36–287（252 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.96 Å R-free 0.250
1TKW The transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR Deposited 2004-06-09	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 36–287（252 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYF_BRARA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–250； UniProt 36–285

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	2pcf
Deposition date deposition_date	1997-12-22
Structure title title	THE COMPLEX OF CYTOCHROME F AND PLASTOCYANIN DETERMINED WITH PARAMAGNETIC NMR. BASED ON THE STRUCTURES OF CYTOCHROME F AND PLASTOCYANIN, 10 STRUCTURES
Keywords keywords	;ELECTRON TRANSPORT, PARAMAGNETIC, CHEMICAL SHIFT, COMPLEX FORMATION, DYNAMIC COMPLEX, PHOTOSYNTHESIS, PSEUDOCONTACT SHIFT, COMPLEX (ELECTRON TRANSPORT PROTEINS) ;; COMPLEX (ELECTRON TRANSPORT PROTEINS)
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	23.51 Å
Radius of gyration Rg (electron density) rg_electron	23.73 Å
Forward intensity I(0) i0	1959600000.00
Molecular weight molecular_weight	383740.0 kDa
Excluded volume excluded_volume	483150 Å³
Envelope volume envelope_volume	63967 Å³
Hydration-shell volume shell_volume	23401 Å³
Envelope diameter envelope_diameter	89.3 Å
Shell Rg shell_rg	30.11 Å
Envelope Rg envelope_rg	24.60 Å
Shape Rg shape_rg	23.72 Å
Total Rg total_rg	23.88 Å
Total atoms total_atoms	53890
Residues n_residues	3490
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	78.1 Å
Rg (real space) rg_real	23.67 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.9600e+09
I(0) uncertainty (real space) i0_real_error	3.2790e+07
Rg (reciprocal space) rg_reciprocal	23.63 Å
I(0) (reciprocal space) i0_reciprocal	1960000000.0000
Solution quality estimate total_estimate	0.8776
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.0 Å
Skewness Skewness skewness	0.528
Kurtosis Kurtosis kurtosis	-0.146
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3910000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.899; Smooth: 0.958

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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	10420.6 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	53890

VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN

来源 Source

来源生物 organism	Spinacia oleracea
通用名 common_name	spinach
NCBI Class编号 ncbi_taxonomy_id	3562
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	CYTOCHROME F
Molecular weight formula_weight	27318.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

YPIFAQQNYENPREATGRIVCANCHLASKPVDIEVPQAVLPDTVFEAVVKIPYDMQLKQVLANGKKGALNVGAVLILPEGFELAPPDRISPEMKEKIGNLSFQNYRPNKKNILVIGPVPGQKYSEITFPILAPDPATNKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATAGGIISKILRKEKGGYEITIVDASNERQVIDIIPRGLELLVSEGESIKLDQPLTSNPNVGGFGQGDAEIVLQDPLR

来源 Source

来源生物 organism	Brassica rapa
NCBI Class编号 ncbi_taxonomy_id	3711
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2pcfa_
Class class	i — Low resolution protein structures
Fold Fold fold	i.4 — Electron transport chains
Superfamily Superfamily superfamily	i.4.1 — Electron transport chains
Family Family family	i.4.1.1 — Electron transport chains

Domain ID domain_id	d2pcfb_
Class class	i — Low resolution protein structures
Fold Fold fold	i.4 — Electron transport chains
Superfamily Superfamily superfamily	i.4.1 — Electron transport chains
Family Family family	i.4.1.1 — Electron transport chains

CATH v4.4 (3 domains)

Domain ID domain_id	2pcfA00
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	2pcfB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	830 — Cytochrome f large domain

Domain ID domain_id	2pcfB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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8. Citations (3)

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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	—

fit	/app/data/saxs_computation/pc/2pcf/2pcf.fit
pddf	/app/data/pr_computation/pc/2pcf/2pcf.pr.out
profile	/app/data/saxs_computation/pc/2pcf/2pcf.dat

THE COMPLEX OF CYTOCHROME F AND PLASTOCYANIN DETERMINED WITH PARAMAGNETIC NMR. BASED ON THE STRUCTURES OF CYTOCHROME F AND PLASTOCYANIN, 10 STRUCTURES

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

CYTOCHROME F

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)