SAXSdb — 1a8c

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

FERROCYTOCHROME C-552

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 23–103	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions：pH 6.9；323 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1 NMR sample composition：WATER	Resolution not provided

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 1A8C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A56 PRIMARY SEQUENCE AND SOLUTION CONFORMATION OF FERRICYTOCHROME C-552 FROM NITROSOMONAS EUROPAEA, NMR, MEAN STRUCTURE REFINED WITH EXPLICIT HYDROGEN BOND CONSTRAINTS Deposited 1998-02-20	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–103（81 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 6.9；323 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1 NMR sample composition WATER	Resolution not provided
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 13 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain M 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 14 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain N 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 15 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain O 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 16 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 17 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain Q 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 18 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOW Crystal Structure of Wild Type Nitrosomonas europaea Cytochrome c552 Deposited 2013-02-25	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 23–103（81 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；3 M AMMONIUM SULFATE, 10 MM TRIS-HCL PH 8	Resolution 2.35 Å R-free 0.258
3ZOX Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (monoclinic space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；0.1 M CHES PH 9.5, 30% (W/V) PEG 8000	Resolution 2.10 Å R-free 0.274
3ZOX Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (monoclinic space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；0.1 M CHES PH 9.5, 30% (W/V) PEG 8000	Resolution 2.10 Å R-free 0.274
3ZOX Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (monoclinic space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；0.1 M CHES PH 9.5, 30% (W/V) PEG 8000	Resolution 2.10 Å R-free 0.274
3ZOX Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (monoclinic space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9.5；0.1 M CHES PH 9.5, 30% (W/V) PEG 8000	Resolution 2.10 Å R-free 0.274
3ZOY Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.226
3ZOY Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.226
3ZOY Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.226
3ZOY Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal space group) Deposited 2013-02-26	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 23–103（81 aa）	Mutation：YES	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1 M TRIS-HCL PH 8.5, 3.1 M AMMONIUM SULFATE	Resolution 2.30 Å R-free 0.226
4JCG Recombinant wild type Nitrosomonas europaea cytochrome c552 Deposited 2013-02-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–103（81 aa） Fragment：Cyt C552 (UNP Residues 23-103)	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；19% (w/v) PEG 6000, 0.2 M LiCl, 0.1 M Tris-HCl pH 7.4 at 7-8 mM protein concentration., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.63 Å R-free 0.234

5 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C552_NITEU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–81； UniProt 23–103

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	1a8c
Deposition date deposition_date	1998-03-23
Structure title title	PRIMARY SEQUENCE AND SOLUTION CONFORMATION OF FERROCYTOCHROME C-552 FROM NITROSOMONAS EUROPAEA, NMR, MEAN STRUCTURE REFINED WITHOUT HYDROGEN BOND CONSTRAINTS
Keywords keywords	HEMOPROTEIN, CYTOCHROME, PROKARYOTIC ELECTRON TRANSPORT; HEMOPROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	12.99 Å
Radius of gyration Rg (electron density) rg_electron	11.50 Å
Forward intensity I(0) i0	1753650.00
Molecular weight molecular_weight	9099.0 kDa
Excluded volume excluded_volume	11476 Å³
Envelope volume envelope_volume	12601 Å³
Hydration-shell volume shell_volume	9359 Å³
Envelope diameter envelope_diameter	38.2 Å
Shell Rg shell_rg	17.17 Å
Envelope Rg envelope_rg	11.87 Å
Shape Rg shape_rg	11.48 Å
Total Rg total_rg	13.03 Å
Total atoms total_atoms	1273
Residues n_residues	81
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	39.3 Å
Rg (real space) rg_real	12.89 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	1.7540e+06
I(0) uncertainty (real space) i0_real_error	1.7370e+04
Rg (reciprocal space) rg_reciprocal	12.90 Å
I(0) (reciprocal space) i0_reciprocal	1754000.0000
Solution quality estimate total_estimate	0.8980
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.4 Å
Skewness Skewness skewness	0.054
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	304100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a8ca_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (1 domains)

Domain ID domain_id	1a8cA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	FERROCYTOCHROME C-552
Molecular weight formula_weight	8491.7 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	1273

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

PRIMARY SEQUENCE AND SOLUTION CONFORMATION OF FERROCYTOCHROME C-552 FROM NITROSOMONAS EUROPAEA, NMR, MEAN STRUCTURE REFINED WITHOUT HYDROGEN BOND CONSTRAINTS

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

FERROCYTOCHROME C-552

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/a8/1a8c/1a8c.fit
pddf	/app/data/pr_computation/a8/1a8c/1a8c.pr.out
profile	/app/data/saxs_computation/a8/1a8c/1a8c.dat