SAXSdb — 1ewh

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

CYTOCHROME F

Chlamydomonas reinhardtii

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 32–282	Fragment：N-TERMINAL SOLUBLE FRAGMENT	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 32–282	Fragment：N-TERMINAL SOLUBLE FRAGMENT	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 32–282	Fragment：N-TERMINAL SOLUBLE FRAGMENT	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

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 1EWH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CFM CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII Deposited 1998-09-18	Different construct Different mutation/modification 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 32–282（251 aa） Chain B 32–282（251 aa） Chain C 32–282（251 aa）	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
1E2V N153Q mutant of cytochrome f from Chlamydomonas reinhardtii Deposited 2000-05-29	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 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 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 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 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 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 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 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 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
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 11 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	1ewh
Deposition date deposition_date	2000-04-25
Structure title title	STRUCTURE OF CYTOCHROME F FROM CHLAMYDOMONAS REINHARDTII
Keywords keywords	BETA SANDWICH, HEME PROTEIN, 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	34.19 Å
Radius of gyration Rg (electron density) rg_electron	34.02 Å
Forward intensity I(0) i0	103583000.00
Molecular weight molecular_weight	83377.0 kDa
Excluded volume excluded_volume	105500 Å³
Envelope volume envelope_volume	144900 Å³
Hydration-shell volume shell_volume	37565 Å³
Envelope diameter envelope_diameter	129.8 Å
Shell Rg shell_rg	38.15 Å
Envelope Rg envelope_rg	34.02 Å
Shape Rg shape_rg	34.00 Å
Total Rg total_rg	34.47 Å
Total atoms total_atoms	5881
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	120.5 Å
Rg (real space) rg_real	34.34 Å
Rg uncertainty (real space) rg_real_error	1.59 Å
I(0) (real space) i0_real	1.0360e+08
I(0) uncertainty (real space) i0_real_error	1.7330e+06
Rg (reciprocal space) rg_reciprocal	34.25 Å
I(0) (reciprocal space) i0_reciprocal	103600000.0000
Solution quality estimate total_estimate	0.8562
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.9 Å
Skewness Skewness skewness	0.511
Kurtosis Kurtosis kurtosis	-0.028
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7339000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.934

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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	CYTOCHROME F
Molecular weight formula_weight	27182.0 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	6602

YPVFAQQNYANPREANGRIVCANCHLAQKAVEIEVPQAVLPDTVFEAVIELPYDKQVKQVLANGKKGDLNVGMVLILPEGFELAPPDRVPAEIKEKVGNLYYQPYSPEQKNILVVGPVPGKKYSEMVVPILSPDPAKNKNVSYLKYPIYFGGNRGRGQVYPDGKKSNNTIYNASAAGKIVAITALSEKKGGFEVSIEKANGEVVVDKIPAGPDLIVKEGQTVQADQPLTNNPNVGGFGQAETEIVLQNPAR

来源 Source

来源生物 organism	Chlamydomonas reinhardtii
NCBI Class编号 ncbi_taxonomy_id	3055
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	721

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1ewha1
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	d1ewha2
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	d1ewhb1
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	d1ewhb2
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	d1ewhc1
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	d1ewhc2
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	1ewhA01
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	1ewhA02
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	1ewhB01
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	1ewhB02
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	1ewhC01
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	1ewhC02
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	76.450 Å
Unit-cell length b length_b	94.300 Å
Unit-cell length c length_c	119.900 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	2.350 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2560

fit	/app/data/saxs_computation/ew/1ewh/1ewh.fit
pddf	/app/data/pr_computation/ew/1ewh/1ewh.pr.out
profile	/app/data/saxs_computation/ew/1ewh/1ewh.dat

STRUCTURE OF 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