SAXSdb — 1ci3

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

PROTEIN (CYTOCHROME F)

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 M； UniProt 46–294	Fragment：SOLUBLE EXTRINSIC FRAGMENT	ZN ZINC ION × 2 HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 1.90 Å R-free 0.235
2	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain M； UniProt 46–294	Fragment：SOLUBLE EXTRINSIC FRAGMENT	ZN ZINC ION × 12 HEC HEME C × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 1.90 Å R-free 0.235
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 46–294	Fragment：SOLUBLE EXTRINSIC FRAGMENT	ZN ZINC ION × 4 HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 1.90 Å R-free 0.235

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CYF_PHOLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain M； PDBConstruct 1–249； UniProt 46–294

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	1ci3
Deposition date deposition_date	1999-04-07
Structure title title	CYTOCHROME F FROM THE B6F COMPLEX OF PHORMIDIUM LAMINOSUM
Keywords keywords	ELECTRON TRANSFER PROTEIN, COMPLEX SUBUNIT, 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	22.93 Å
Radius of gyration Rg (electron density) rg_electron	22.54 Å
Forward intensity I(0) i0	13097500.00
Molecular weight molecular_weight	27160.0 kDa
Excluded volume excluded_volume	33907 Å³
Envelope volume envelope_volume	41129 Å³
Hydration-shell volume shell_volume	17096 Å³
Envelope diameter envelope_diameter	85.9 Å
Shell Rg shell_rg	27.20 Å
Envelope Rg envelope_rg	23.22 Å
Shape Rg shape_rg	22.53 Å
Total Rg total_rg	23.24 Å
Total atoms total_atoms	1909
Residues n_residues	249
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	84.3 Å
Rg (real space) rg_real	23.26 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	1.3100e+07
I(0) uncertainty (real space) i0_real_error	1.9770e+05
Rg (reciprocal space) rg_reciprocal	23.18 Å
I(0) (reciprocal space) i0_reciprocal	13100000.0000
Solution quality estimate total_estimate	0.7835
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.712
Kurtosis Kurtosis kurtosis	0.090
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2806000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.560; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.519; Smooth: 0.984

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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	PROTEIN (CYTOCHROME F)
Molecular weight formula_weight	26462.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M
Atom count atom_count	2181

YPFWAQQNYANPREATGRIVCANCHLAAKPAEIEVPQAVLPDSVFKAVVKIPYDHSVQQVQADGSKGPLNVGAVLMLPEGFTIAPEDRIPEEMKEEVGPSYLFQPYADDKQNIVLVGPLPGDEYEEIVFPVLSPNPATNKSVAFGKYSIHLGANRGRGQIYPTGEKSNNAVYNASAAGVITAIAKADDGSAEVKIRTEDGTTIVDKIPAGPELIVSEGEEVAAGAALTNNPNVGGFGQKDTEIVLQSPN

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 str. K12 substr. W3110

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 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	250

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ci3m1
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	d1ci3m2
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 (2 domains)

Domain ID domain_id	1ci3M01
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	1ci3M02
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 (2)

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Unit-cell length a length_a	109.600 Å
Unit-cell length b length_b	109.600 Å
Unit-cell length c length_c	145.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2030
R_free r_free	0.2350

fit	/app/data/saxs_computation/ci/1ci3/1ci3.fit
pddf	/app/data/pr_computation/ci/1ci3/1ci3.pr.out
profile	/app/data/saxs_computation/ci/1ci3/1ci3.dat

CYTOCHROME F FROM THE B6F COMPLEX OF PHORMIDIUM LAMINOSUM

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

PROTEIN (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