SAXSdb — 1ql3

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

CYTOCHROME C552

PARACOCCUS DENITRIFICANS

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 78–176	Fragment：SOLUBLE DOMAIN	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.50	Resolution 1.40 Å R-free 0.242
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 78–176	Fragment：SOLUBLE DOMAIN	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.50	Resolution 1.40 Å R-free 0.242
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 78–176	Fragment：SOLUBLE DOMAIN	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.50	Resolution 1.40 Å R-free 0.242
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 78–176	Fragment：SOLUBLE DOMAIN	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；pH 4.50	Resolution 1.40 Å R-free 0.242

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 1QL3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C7M SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE Deposited 2000-03-03	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–176（99 aa） Fragment：SOLUBLE FUNCTIONAL DOMAIN	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 5.5；298 K NMR sample composition 20 MM PHOSPHATE, 90% H2O/ 10% D2O	Resolution not provided
1I6D SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE Deposited 2001-03-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–176（99 aa） Fragment：SOLUBLE FUNCTIONAL DOMAIN	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 5.5；298 K NMR sample composition 20 MM PHOSPHATE, 90% H2O/ 10% D2O	Resolution not provided
1I6E SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE OXIDIZED STATE Deposited 2001-03-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–176（99 aa） Fragment：SOLUBLE FUNCTIONAL DOMAIN	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 5.5；298 K NMR sample composition 20 MM PHOSPHATE, 90% H2O/ 10% D2O	Resolution not provided
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–176（99 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.50	Resolution 1.50 Å R-free 0.268
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 78–176（99 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.50	Resolution 1.50 Å R-free 0.268
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20	Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 78–176（99 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.50	Resolution 1.50 Å R-free 0.268
1QL4 Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the oxidised state Deposited 1999-08-20	Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 78–176（99 aa） Fragment：SOLUBLE DOMAIN	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.50	Resolution 1.50 Å R-free 0.268
3M97 Structure of the soluble domain of cytochrome c552 with its flexible linker segment from Paracoccus denitrificans Deposited 2010-03-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 38–176（139 aa） Fragment：soluble domain with flexible linker segment (UNP residues 38-176)	Not recorded	HEC HEME C × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20 % PEG 550 MME, 0.1 M Zinc sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.33 Å R-free 0.229

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C552_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 78–176 Author chain B； PDBConstruct 1–99； UniProt 78–176 Author chain C； PDBConstruct 1–99； UniProt 78–176 Author chain D； PDBConstruct 1–99； UniProt 78–176

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	1ql3
Deposition date deposition_date	1999-08-20
Structure title title	Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state
Keywords keywords	ELECTRON TRANSPORT PROTEIN (CYTOCHROME), ELECTRON TRANSFER, REDUCED; ELECTRON TRANSPORT PROTEIN (CYTOCHROME)
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	27.96 Å
Radius of gyration Rg (electron density) rg_electron	27.89 Å
Forward intensity I(0) i0	32575400.00
Molecular weight molecular_weight	44105.0 kDa
Excluded volume excluded_volume	55022 Å³
Envelope volume envelope_volume	67228 Å³
Hydration-shell volume shell_volume	22401 Å³
Envelope diameter envelope_diameter	100.7 Å
Shell Rg shell_rg	31.72 Å
Envelope Rg envelope_rg	27.75 Å
Shape Rg shape_rg	27.88 Å
Total Rg total_rg	28.33 Å
Total atoms total_atoms	3100
Residues n_residues	396
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	94.9 Å
Rg (real space) rg_real	28.33 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	3.2580e+07
I(0) uncertainty (real space) i0_real_error	5.3370e+05
Rg (reciprocal space) rg_reciprocal	28.22 Å
I(0) (reciprocal space) i0_reciprocal	32570000.0000
Solution quality estimate total_estimate	0.7494
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.564
Kurtosis Kurtosis kurtosis	-0.252
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16420000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.640; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME C552
Molecular weight formula_weight	10422.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3680

ADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ

来源 Source

来源生物 organism	PARACOCCUS DENITRIFICANS
NCBI Class编号 ncbi_taxonomy_id	266
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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	580

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ql3a_
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

Domain ID domain_id	d1ql3b_
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

Domain ID domain_id	d1ql3c_
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

Domain ID domain_id	d1ql3d_
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 (4 domains)

Domain ID domain_id	1ql3A00
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

Domain ID domain_id	1ql3B00
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

Domain ID domain_id	1ql3C00
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

Domain ID domain_id	1ql3D00
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	53.690 Å
Unit-cell length b length_b	54.320 Å
Unit-cell length c length_c	140.740 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2420

fit	/app/data/saxs_computation/ql/1ql3/1ql3.fit
pddf	/app/data/pr_computation/ql/1ql3/1ql3.pr.out
profile	/app/data/saxs_computation/ql/1ql3/1ql3.dat

Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the reduced state

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