SAXSdb — 1rfs

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

RIESKE PROTEIN

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 A； UniProt 109–247	Fragment：SOLUBLE FRAGMENT, C-TERMINAL RESIDUES 41 - 179	FES FE2/S2 (INORGANIC) CLUSTER × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.83 Å R-free 0.220

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 1RFS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6RQF 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules Deposited 2019-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D 52–230（179 aa） Chain L 52–230（179 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 BCR BETA-CAROTENE × 2 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 × 3 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
7QRM Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution Deposited 2022-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D 1–230（230 aa） Chain L 1–230（230 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 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 UMQ UNDECYL-MALTOSIDE × 10 PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7ZYV Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution Deposited 2022-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain D 1–230（230 aa） Chain L 1–230（230 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 10 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 × 6 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Buffer and the diluted protein sample were filtered through a 0.22 um syringe filter. Prior to freezing, protein sample was concentrated on centrifugal filter units with 50K MWCO. cryo-EM vitrification conditions Cryogen ETHANE；blot time 2 s, wait time 0 s, blot force -1	Resolution 2.13 Å
9ES7 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution Deposited 2024-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric	Chain D 1–230（230 aa） Chain L 1–230（230 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.94 Å
9ES8 Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at plastoquionol reduction site Deposited 2024-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain D 1–230（230 aa） Chain L 1–230（230 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 A1H65 Decylplastoquinone × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 CLA CHLOROPHYLL A × 2 UMQ UNDECYL-MALTOSIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7；final concentration of plastocyanin was 0.34 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.24 Å
9ES9 Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site Deposited 2024-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: 18-meric	Chain D 1–230（230 aa） Chain L 1–230（230 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 4 UMQ UNDECYL-MALTOSIDE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 BNT 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE × 2 CLA CHLOROPHYLL A × 2 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 BCR BETA-CAROTENE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.33 Å
9TGG Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin Deposited 2025-12-01	Different construct Different mutation/modification 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 D 52–230（179 aa） Chain L 52–230（179 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

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UCRIA_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 109–247

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	1rfs
Deposition date deposition_date	1997-08-14
Structure title title	RIESKE SOLUBLE FRAGMENT FROM SPINACH
Keywords keywords	IRON-SULFUR PROTEIN, ELECTRON TRANSPORT; IRON-SULFUR PROTEIN
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	15.25 Å
Radius of gyration Rg (electron density) rg_electron	14.08 Å
Forward intensity I(0) i0	4004730.00
Molecular weight molecular_weight	13839.0 kDa
Excluded volume excluded_volume	17132 Å³
Envelope volume envelope_volume	19022 Å³
Hydration-shell volume shell_volume	11696 Å³
Envelope diameter envelope_diameter	49.0 Å
Shell Rg shell_rg	19.50 Å
Envelope Rg envelope_rg	14.32 Å
Shape Rg shape_rg	14.01 Å
Total Rg total_rg	15.35 Å
Total atoms total_atoms	1168
Residues n_residues	127
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	50.5 Å
Rg (real space) rg_real	15.16 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	4.0050e+06
I(0) uncertainty (real space) i0_real_error	4.7120e+04
Rg (reciprocal space) rg_reciprocal	15.17 Å
I(0) (reciprocal space) i0_reciprocal	4005000.0000
Solution quality estimate total_estimate	0.8889
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.2 Å
Skewness Skewness skewness	0.146
Kurtosis Kurtosis kurtosis	-0.405
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	520600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1rfsa_
Class class	b — All beta proteins
Fold Fold fold	b.33 — ISP domain
Superfamily Superfamily superfamily	b.33.1 — ISP domain
Family Family family	b.33.1.1 — Rieske iron-sulfur protein (ISP)

CATH v4.4 (1 domains)

Domain ID domain_id	1rfsA00
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

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8. Citations (2)

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Unit-cell length a length_a	29.050 Å
Unit-cell length b length_b	31.870 Å
Unit-cell length c length_c	35.790 Å
Unit-cell angle α angle_alpha	95.60 °
Unit-cell angle β angle_beta	106.10 °
Unit-cell angle γ angle_gamma	117.30 °
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	—

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1700
R_work r_work	0.1700
R_free r_free	0.2200

Description description	RIESKE PROTEIN
Molecular weight formula_weight	14636.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1597

RIESKE SOLUBLE FRAGMENT FROM SPINACH

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

RIESKE PROTEIN

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

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)

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	143

fit	/app/data/saxs_computation/rf/1rfs/1rfs.fit
pddf	/app/data/pr_computation/rf/1rfs/1rfs.pr.out
profile	/app/data/saxs_computation/rf/1rfs/1rfs.dat