SAXSdb — 1a7v

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

;CYTOCHROME C' ;

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 1–125	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.30 Å R-free 0.241
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–125	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.30 Å R-free 0.241

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 1A7V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MQV Crystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas palustris cytochrome c' (prime) expressed in E. coli Deposited 2002-09-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–125（125 aa）	Mutation：Q1A, F32W, W72F	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.78 Å R-free 0.265
1MQV Crystal Structure of the Q1A/F32W/W72F mutant of Rhodopseudomonas palustris cytochrome c' (prime) expressed in E. coli Deposited 2002-09-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–125（125 aa）	Mutation：Q1A, F32W, W72F	HEC HEME C × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG6000, sodium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.78 Å R-free 0.265

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

View Construct and Data Evidence

UniProt name	CYCP_RHOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 1–125 Author chain B； PDBConstruct 1–125； UniProt 1–125

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	1a7v
Deposition date deposition_date	1998-03-18
Structure title title	CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS
Keywords keywords	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	21.21 Å
Radius of gyration Rg (electron density) rg_electron	20.43 Å
Forward intensity I(0) i0	13032400.00
Molecular weight molecular_weight	27503.0 kDa
Excluded volume excluded_volume	34718 Å³
Envelope volume envelope_volume	40903 Å³
Hydration-shell volume shell_volume	17630 Å³
Envelope diameter envelope_diameter	73.2 Å
Shell Rg shell_rg	26.05 Å
Envelope Rg envelope_rg	20.85 Å
Shape Rg shape_rg	20.40 Å
Total Rg total_rg	21.39 Å
Total atoms total_atoms	1928
Residues n_residues	250
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	76.7 Å
Rg (real space) rg_real	21.27 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.3030e+07
I(0) uncertainty (real space) i0_real_error	2.0440e+05
Rg (reciprocal space) rg_reciprocal	21.26 Å
I(0) (reciprocal space) i0_reciprocal	13030000.0000
Solution quality estimate total_estimate	0.8389
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.433
Kurtosis Kurtosis kurtosis	-0.203
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4225000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.796; Smooth: 1.000

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1a7va_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

Domain ID domain_id	d1a7vb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.3 — Cytochromes
Family Family family	a.24.3.2 — Cytochrome c'-like

CATH v4.4 (2 domains)

Domain ID domain_id	1a7vA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	10 — Cytochrome c/b562

Domain ID domain_id	1a7vB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	10 — Cytochrome c/b562

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8. Citations (1)

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Unit-cell length a length_a	63.000 Å
Unit-cell length b length_b	113.500 Å
Unit-cell length c length_c	34.500 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	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2410

Description description	;CYTOCHROME C' ;
Molecular weight formula_weight	13152.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2123

CYTOCHROME C' FROM RHODOPSEUDOMONAS PALUSTRIS

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

;CYTOCHROME C' ;

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

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	2

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	195

fit	/app/data/saxs_computation/a7/1a7v/1a7v.fit
pddf	/app/data/pr_computation/a7/1a7v/1a7v.pr.out
profile	/app/data/saxs_computation/a7/1a7v/1a7v.dat