SAXSdb — 1cfm

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

CYTOCHROME F

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 32–282 Chain B； UniProt 32–282 Chain C； UniProt 32–282	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.271

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 1CFM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1E2V N153Q mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–282（251 aa）	Mutation：YES	HEC HEME C × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000.	Resolution 1.85 Å R-free 0.219
1E2V N153Q mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 32–282（251 aa）	Mutation：YES	HEC HEME C × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000.	Resolution 1.85 Å R-free 0.219
1E2V N153Q mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 32–282（251 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 6.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.5, 25 MM CALCIUM ACETATE, 1 MM DTT AND 17-19% PEG 8000.	Resolution 1.85 Å R-free 0.219
1E2W N168F mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–282（251 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, PH 7.5, 1 MM DTT, THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 200 MM AMMONIUM FORMATE, 14% GLYCEROL, 17% PEG-3350.	Resolution 1.60 Å R-free 0.226
1E2W N168F mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 32–282（251 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, PH 7.5, 1 MM DTT, THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 200 MM AMMONIUM FORMATE, 14% GLYCEROL, 17% PEG-3350.	Resolution 1.60 Å R-free 0.226
1E2Z Q158L mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–282（251 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 7.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 50 MM AMMONIUM FLUORIDE 5% GLYCEROL AND 19-21% PEG 3350.	Resolution 2.50 Å R-free 0.279
1E2Z Q158L mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 32–282（251 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 7.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 50 MM AMMONIUM FLUORIDE 5% GLYCEROL AND 19-21% PEG 3350.	Resolution 2.50 Å R-free 0.279
1E2Z Q158L mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 32–282（251 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；THE PROTEIN WAS BUFFERED IN 10 MM NA2HPO4/NAH2PO4, 1 MM DTT, PH 7.5 AND THE RESERVOIR CONTAINED 100 MM MES, PH 6.7, 50 MM AMMONIUM FLUORIDE 5% GLYCEROL AND 19-21% PEG 3350.	Resolution 2.50 Å R-free 0.279
1EWH STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII Deposited 2000-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 32–282（251 aa） Fragment：N-TERMINAL SOLUBLE FRAGMENT	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, calcium acetate, MES, pH 6.5, VAPOR DIFFUSION, temperature 20K	Resolution 2.35 Å R-free 0.256
1EWH STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII Deposited 2000-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 32–282（251 aa） Fragment：N-TERMINAL SOLUBLE FRAGMENT	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, calcium acetate, MES, pH 6.5, VAPOR DIFFUSION, temperature 20K	Resolution 2.35 Å R-free 0.256
1EWH STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII Deposited 2000-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 32–282（251 aa） Fragment：N-TERMINAL SOLUBLE FRAGMENT	Not recorded	HEC HEME C × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, calcium acetate, MES, pH 6.5, VAPOR DIFFUSION, temperature 20K	Resolution 2.35 Å R-free 0.256
1Q90 Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii Deposited 2003-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 32–317（286 aa） Fragment：Residues 1-292	Mutation：6 His tag at C-terminus	HEC HEME C × 8 BCR BETA-CAROTENE × 2 LFA EICOSANE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 2 CLA CHLOROPHYLL A × 2 TDS 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE × 2 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 4 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.261
1Q90 Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii Deposited 2003-08-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 32–317（286 aa） Fragment：Residues 1-292	Mutation：6 His tag at C-terminus	HEC HEME C × 16 BCR BETA-CAROTENE × 4 LFA EICOSANE × 4 FES FE2/S2 (INORGANIC) CLUSTER × 4 CLA CHLOROPHYLL A × 4 TDS 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE × 4 LMG 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 8 SQD 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.261

5 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYF_CHLRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–251； UniProt 32–282 Author chain B； PDBConstruct 1–251； UniProt 32–282 Author chain C； PDBConstruct 1–251； UniProt 32–282

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	1cfm
Deposition date deposition_date	1998-09-18
Structure title title	CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
Keywords keywords	CYTOCHROME F, PLASTOCYANIN, PROTON WIRE, HEME, 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	35.59 Å
Radius of gyration Rg (electron density) rg_electron	35.76 Å
Forward intensity I(0) i0	102069000.00
Molecular weight molecular_weight	83312.0 kDa
Excluded volume excluded_volume	105400 Å³
Envelope volume envelope_volume	141810 Å³
Hydration-shell volume shell_volume	35638 Å³
Envelope diameter envelope_diameter	140.7 Å
Shell Rg shell_rg	39.05 Å
Envelope Rg envelope_rg	35.65 Å
Shape Rg shape_rg	35.74 Å
Total Rg total_rg	36.09 Å
Total atoms total_atoms	5877
Residues n_residues	753
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	127.1 Å
Rg (real space) rg_real	35.84 Å
Rg uncertainty (real space) rg_real_error	1.32 Å
I(0) (real space) i0_real	1.0210e+08
I(0) uncertainty (real space) i0_real_error	1.6950e+06
Rg (reciprocal space) rg_reciprocal	35.69 Å
I(0) (reciprocal space) i0_reciprocal	102100000.0000
Solution quality estimate total_estimate	0.8429
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.7 Å
Skewness Skewness skewness	0.480
Kurtosis Kurtosis kurtosis	-0.313
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8455000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.751; Smooth: 0.887

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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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1cfma1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.6 — Cytochrome f, large domain
Family Family family	b.2.6.1 — Cytochrome f, large domain

Domain ID domain_id	d1cfma2
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
Family Family family	b.84.2.2 — Cytochrome f, small domain

Domain ID domain_id	d1cfmb1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.6 — Cytochrome f, large domain
Family Family family	b.2.6.1 — Cytochrome f, large domain

Domain ID domain_id	d1cfmb2
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
Family Family family	b.84.2.2 — Cytochrome f, small domain

Domain ID domain_id	d1cfmc1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.6 — Cytochrome f, large domain
Family Family family	b.2.6.1 — Cytochrome f, large domain

Domain ID domain_id	d1cfmc2
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.2 — Rudiment single hybrid motif
Family Family family	b.84.2.2 — Cytochrome f, small domain

CATH v4.4 (6 domains)

Domain ID domain_id	1cfmA01
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	1cfmA02
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

Domain ID domain_id	1cfmB01
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	1cfmB02
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

Domain ID domain_id	1cfmC01
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	1cfmC02
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 (1)

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Unit-cell length a length_a	75.624 Å
Unit-cell length b length_b	94.943 Å
Unit-cell length c length_c	119.920 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2710

Description description	CYTOCHROME F
Molecular weight formula_weight	27182.0 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6878

CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII

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

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

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	3

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1001

fit	/app/data/saxs_computation/cf/1cfm/1cfm.fit
pddf	/app/data/pr_computation/cf/1cfm/1cfm.pr.out
profile	/app/data/saxs_computation/cf/1cfm/1cfm.dat