SAXSdb — 1b7v

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

PROTEIN (CYTOCHROME C-553)

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 22–92	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；8MG/ML OF CYTOCHROME, 20MM TRIS.HCL, PH 8.0 AT 20 DEGREES C, HANGING DROPS IN HAMPTON RESEARCH 24-WELL LINBRO PLATES, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.206

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 1B7V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C75 0.97 A "AB INITIO" CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BACILLUS PASTEURII Deposited 2000-02-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–92（71 aa）	Not recorded	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；3.2 M AMMONIUM SULPHATE IN 100 MM SODIUM CITRATE BUFFER PH 5.0	Resolution 0.97 Å
1K3G NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii Deposited 2001-10-03	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–92（71 aa） Fragment：residues 22-92	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7.5；288 K；Ionic strength (raw mmCIF value) 10 mM phosphate buffer；Pressure Ambient NMR sample composition 1-3 mM oxidized cytochrome c-553 in 10 mM phosphate buffer \| 90%H2O+10%D2O; 100% D2O	Resolution not provided
1K3H NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii Deposited 2001-10-03	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–92（71 aa） Fragment：RESIDUES 22-92	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7.5；288 K；Ionic strength (raw mmCIF value) 10 mM phosphate buffer；Pressure Ambient NMR sample composition 1-3 mM oxidized cytochrome c-553 in 10 mM phosphate buffer \| 90%H2O+10%D2O; 100% D2O	Resolution not provided
1N9C Structure and dynamics of reduced Bacillus pasteurii cytochrome c: oxidation state dependent properties and implications for electron transfer processes Deposited 2002-11-23	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–92（71 aa） Fragment：soluble part of membrane-anchored cytochrome c	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 100 mM Pi；Pressure ambient NMR sample composition 2 mM cytochrome, 100mM phosphate buffer, pH 7.0 \| 90% H2O/10% D2O NMR sample composition 1 mM cytochrome U-15N, 100mM phosphate buffer, pH 7.0 \| 90% H2O/10% D2O	Resolution not provided

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CY553_BACPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–71； UniProt 22–92

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	1b7v
Deposition date deposition_date	1999-01-22
Structure title title	Structure of the C-553 cytochrome from Bacillus pasteruii to 1.7 A resolution
Keywords keywords	CYTOCHROME, ELECTRON TRANSFER; ELECTRON TRANSFER
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	11.96 Å
Radius of gyration Rg (electron density) rg_electron	10.48 Å
Forward intensity I(0) i0	1337260.00
Molecular weight molecular_weight	7705.0 kDa
Excluded volume excluded_volume	9573 Å³
Envelope volume envelope_volume	9919 Å³
Hydration-shell volume shell_volume	8188 Å³
Envelope diameter envelope_diameter	34.3 Å
Shell Rg shell_rg	15.92 Å
Envelope Rg envelope_rg	10.72 Å
Shape Rg shape_rg	10.47 Å
Total Rg total_rg	11.86 Å
Total atoms total_atoms	539
Residues n_residues	71
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	35.6 Å
Rg (real space) rg_real	11.85 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.3370e+06
I(0) uncertainty (real space) i0_real_error	1.4550e+04
Rg (reciprocal space) rg_reciprocal	11.85 Å
I(0) (reciprocal space) i0_reciprocal	1337000.0000
Solution quality estimate total_estimate	0.8871
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.1 Å
Skewness Skewness skewness	-0.033
Kurtosis Kurtosis kurtosis	-0.388
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	251000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.904

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b7va_
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	1b7vA00
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 (3)

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Unit-cell length a length_a	37.090 Å
Unit-cell length b length_b	39.160 Å
Unit-cell length c length_c	43.990 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1740
R_work r_work	0.1740
R_free r_free	0.2060

Description description	PROTEIN (CYTOCHROME C-553)
Molecular weight formula_weight	7115.9 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	667

Structure of the C-553 cytochrome from Bacillus pasteruii to 1.7 A resolution

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

PROTEIN (CYTOCHROME C-553)

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

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 (3)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	HEME C
Molecular weight formula_weight	618.5 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	128

fit	/app/data/saxs_computation/b7/1b7v/1b7v.fit
pddf	/app/data/pr_computation/b7/1b7v/1b7v.pr.out
profile	/app/data/saxs_computation/b7/1b7v/1b7v.dat