SAXSdb — 1ft5

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

CYTOCHROME C554

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 25–235	Not recorded	PO4 PHOSPHATE ION × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.1；295 K；62.5% w/vol potassium phosphate pH 10.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.215

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 1FT5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BVB HEME-PACKING MOTIFS REVEALED BY THE CRYSTAL STRUCTURE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA Deposited 1998-09-16	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–235（211 aa）	Not recorded	PO4 PHOSPHATE ION × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 10.1；pH 10.1	Resolution 2.60 Å R-free 0.254
1FT6 REDUCED STATE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA Deposited 2000-09-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–235（211 aa）	Not recorded	SO3 SULFITE ION × 1 PO4 PHOSPHATE ION × 1 HEC HEME C × 4 DTN DITHIONITE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.1；295 K；62.5% w/vol potassium phosphate pH 10.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.236

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C554_NITEU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 25–235

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	1ft5
Deposition date deposition_date	2000-09-11
Structure title title	CRYSTAL STRUCTURE OF THE OXIDIZED STATE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA
Keywords keywords	heme-stacking, 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	18.45 Å
Radius of gyration Rg (electron density) rg_electron	17.73 Å
Forward intensity I(0) i0	13099500.00
Molecular weight molecular_weight	26368.0 kDa
Excluded volume excluded_volume	32591 Å³
Envelope volume envelope_volume	37110 Å³
Hydration-shell volume shell_volume	17560 Å³
Envelope diameter envelope_diameter	66.0 Å
Shell Rg shell_rg	23.85 Å
Envelope Rg envelope_rg	18.18 Å
Shape Rg shape_rg	17.69 Å
Total Rg total_rg	18.73 Å
Total atoms total_atoms	1846
Residues n_residues	211
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	65.7 Å
Rg (real space) rg_real	18.43 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	1.3100e+07
I(0) uncertainty (real space) i0_real_error	1.6150e+05
Rg (reciprocal space) rg_reciprocal	18.43 Å
I(0) (reciprocal space) i0_reciprocal	13100000.0000
Solution quality estimate total_estimate	0.7579
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.397
Kurtosis Kurtosis kurtosis	-0.113
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6096000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.642; Stabil: 0.986; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

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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 C554
Molecular weight formula_weight	23656.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1988

ADAPFEGRKKCSSCHKAQAQSWKDTAHAKAMESLKPNVKKEAKQKAKLDPAKDYTQDKDCVGCHVDGFGQKGGYTIESPKPMLTGVGCESCHGPGRNFRGDHRKSGQAFEKSGKKTPRKDLAKKGQDFHFEERCSACHLNYEGSPWKGAKAPYTPFTPEVDAKYTFKFDEMVKEVKAMHEHYKLEGVFEGEPKFKFHDEFQASAKPAKKGK

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ft5a_
Class class	a — All alpha proteins
Fold Fold fold	a.138 — Multiheme cytochromes
Superfamily Superfamily superfamily	a.138.1 — Multiheme cytochromes
Family Family family	a.138.1.3 — Di-heme elbow motif

CATH v4.4 (1 domains)

Domain ID domain_id	1ft5A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1130 — Flavocytochrome C3; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Flavocytochrome C3; Chain A

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8. Citations (2)

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Unit-cell length a length_a	147.892 Å
Unit-cell length b length_b	147.892 Å
Unit-cell length c length_c	33.913 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1880
R_free r_free	0.2150

fit	/app/data/saxs_computation/ft/1ft5/1ft5.fit
pddf	/app/data/pr_computation/ft/1ft5/1ft5.pr.out
profile	/app/data/saxs_computation/ft/1ft5/1ft5.dat

CRYSTAL STRUCTURE OF THE OXIDIZED STATE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA

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

CYTOCHROME C554

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