SAXSdb — 1nbb

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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 22–150	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NBN N-BUTYL ISOCYANIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.40 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 22–150	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NBN N-BUTYL ISOCYANIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.40 Å

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 1NBB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CPQ CYTOCHROME C' FROM RHODOPSEUDOMONAS CAPSULATA Deposited 1995-08-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–150（129 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.72 Å
1CPR ST. LOUIS CYTOCHROME C' FROM THE PURPLE PHOTOTROPIC BACTERIUM, RHODOBACTER CAPSULATUS Deposited 1996-04-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–150（129 aa）	Not recorded	ZN ZINC ION × 6 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1EKY MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION Deposited 2000-03-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–129（129 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 7mM Cyt c', 15N, 100mM PO4 pH6 \| 90% H20 10% D20	Resolution not provided
1RCP CYTOCHROME C' Deposited 1995-08-23	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–150（129 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å
1RCP CYTOCHROME C' Deposited 1995-08-23	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 22–150（129 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å

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

View Construct and Data Evidence

UniProt name	CYCP_RHOCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 22–150 Author chain B； PDBConstruct 1–129； UniProt 22–150

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	1nbb
Deposition date deposition_date	1996-03-18
Structure title title	N-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C'
Keywords keywords	ELECTRON TRANSPORT, CYTOCHROME, HEME PROTEIN, ELECTRON TRANSPORT (HEME PROTEIN); ELECTRON TRANSPORT (HEME PROTEIN)
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	21.81 Å
Radius of gyration Rg (electron density) rg_electron	21.01 Å
Forward intensity I(0) i0	14023500.00
Molecular weight molecular_weight	27665.0 kDa
Excluded volume excluded_volume	34355 Å³
Envelope volume envelope_volume	41315 Å³
Hydration-shell volume shell_volume	17518 Å³
Envelope diameter envelope_diameter	71.4 Å
Shell Rg shell_rg	26.05 Å
Envelope Rg envelope_rg	21.00 Å
Shape Rg shape_rg	21.04 Å
Total Rg total_rg	21.61 Å
Total atoms total_atoms	1938
Residues n_residues	258
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	72.2 Å
Rg (real space) rg_real	21.92 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.4020e+07
I(0) uncertainty (real space) i0_real_error	1.7550e+05
Rg (reciprocal space) rg_reciprocal	21.90 Å
I(0) (reciprocal space) i0_reciprocal	14020000.0000
Solution quality estimate total_estimate	0.8738
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.5 Å
Skewness Skewness skewness	0.438
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6797000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.964

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;CYTOCHROME C' ;
Molecular weight formula_weight	13154.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2044

ADTKEVLEAREAYFKSLGGSMKAMTGVAKAFDAEAAKVEAAKLEKILATDVAPLFPAGTSSTDLPGQTEAKAAIWANMDDFGAKGKAMHEAGGAVIAAANAGDGAAFGAALQKLGGTCKACHDDYREED

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	N-BUTYL ISOCYANIDE
Molecular weight formula_weight	83.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1nbba_
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	d1nbbb_
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	1nbbA00
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	1nbbB00
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 (3)

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Unit-cell length a length_a	47.734 Å
Unit-cell length b length_b	70.535 Å
Unit-cell length c length_c	89.652 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	87.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1740
R_work r_work	0.1740
R_free r_free	—

fit	/app/data/saxs_computation/nb/1nbb/1nbb.fit
pddf	/app/data/pr_computation/nb/1nbb/1nbb.pr.out
profile	/app/data/saxs_computation/nb/1nbb/1nbb.dat

N-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C'

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