SAXSdb — 1c52

▼

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

CYTOCHROME-C552

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 18–148	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.2；PROTEIN WAS CRYSTALLIZED FROM 2.8 M AMMONIUM SULFATE, 100 MM TRIS/HCL, PH 8.2	Resolution 1.28 Å R-free 0.224

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 1C52	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FOC Cytochrome C557: improperly folded thermus thermophilus C552 Deposited 2000-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 17–148（132 aa） Chain B 17–148（132 aa）	Not recorded	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；42-46% MPEG 2K (w/v), 0.1M Na cacodylate pH 7.0, 50mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 24K	Resolution 3.00 Å R-free 0.423
1QYZ Characterization of the malformed, recombinant cytochrome rC552 Deposited 2003-09-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–148（131 aa）	Not recorded	HCO 2-ACETYL-PROTOPORPHYRIN IX × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；298 K；PEG 5K MME, imidazole-malate buffer, NaCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.40 Å R-free 0.260
1R0Q Characterization of the conversion of the malformed, recombinant cytochrome rc552 to a 2-formyl-4-vinyl (Spirographis) heme Deposited 2003-09-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–148（131 aa）	Not recorded	HFM 2-FORMYL-PROTOPORPHRYN IX × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；298 K；MPEG 5K, imidazole-malate buffer, NaCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.61 Å R-free 0.255
2FWL The cytochrome c552/CuA complex from Thermus thermophilus Deposited 2006-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–131（131 aa）	Not recorded	HEC HEME C × 1 CUA DINUCLEAR COPPER ION × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM phosphate buffer；Pressure ambient NMR sample composition 0.5mM cytochrome c552 U-15N, 20mM phosphate buffer, 2mM CuA domain, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5mM CuA domain U-15N, 20mM phosphate buffer, 2mM cytochrome c552, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
3VNW Crystal structure of cytochrome c552 from Thermus thermophilus at pH 5.44 Deposited 2012-01-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–131（129 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.44；298 K；0.2M Imidazole-Malate, 42% MPEG 5K, pH 5.44, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.97 Å R-free 0.232

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

View Construct and Data Evidence

UniProt name	C552_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 18–148

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c52
Deposition date deposition_date	1997-06-23
Structure title title	THERMUS THERMOPHILUS CYTOCHROME-C552: A NEW HIGHLY THERMOSTABLE CYTOCHROME-C STRUCTURE OBTAINED BY MAD PHASING
Keywords keywords	ELECTRON TRANSPORT PROTEIN, CYTOCHROME-C552, MAD, THERMOSTABILITY; ELECTRON TRANSPORT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	14.92 Å
Radius of gyration Rg (electron density) rg_electron	13.47 Å
Forward intensity I(0) i0	3973980.00
Molecular weight molecular_weight	14779.0 kDa
Excluded volume excluded_volume	18836 Å³
Envelope volume envelope_volume	20238 Å³
Hydration-shell volume shell_volume	12493 Å³
Envelope diameter envelope_diameter	44.7 Å
Shell Rg shell_rg	19.69 Å
Envelope Rg envelope_rg	13.89 Å
Shape Rg shape_rg	13.42 Å
Total Rg total_rg	14.95 Å
Total atoms total_atoms	1275
Residues n_residues	131
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	46.5 Å
Rg (real space) rg_real	14.79 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	3.9740e+06
I(0) uncertainty (real space) i0_real_error	4.5020e+04
Rg (reciprocal space) rg_reciprocal	14.80 Å
I(0) (reciprocal space) i0_reciprocal	3974000.0000
Solution quality estimate total_estimate	0.8814
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.049
Kurtosis Kurtosis kurtosis	-0.362
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1272000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.985

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c52a_
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	1c52A00
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

▶

8. Citations (4)

▶

Unit-cell length a length_a	47.100 Å
Unit-cell length b length_b	47.100 Å
Unit-cell length c length_c	68.820 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	4

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.280 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2240

Description description	CYTOCHROME-C552
Molecular weight formula_weight	14194.6 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	1863

THERMUS THERMOPHILUS CYTOCHROME-C552: A NEW HIGHLY THERMOSTABLE CYTOCHROME-C STRUCTURE OBTAINED BY MAD PHASING

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

CYTOCHROME-C552

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

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	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

fit	/app/data/saxs_computation/c5/1c52/1c52.fit
pddf	/app/data/pr_computation/c5/1c52/1c52.pr.out
profile	/app/data/saxs_computation/c5/1c52/1c52.dat