SAXSdb — 3x39

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

Cytochrome c-551

Pseudomonas aeruginosa PAO1

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–104	Fragment：UNP residues 23-104	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES-NaOH buffer containing 1.4M sodium citrate tribasic dehydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.50 Å R-free 0.188
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 23–104	Fragment：UNP residues 23-104	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES-NaOH buffer containing 1.4M sodium citrate tribasic dehydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.50 Å R-free 0.188

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 3X39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DVV SOLUTION STRUCTURE OF THE QUINTUPLE MUTANT OF CYTOCHROME C-551 FROM PSEUDOMONAS AERUGINOSA Deposited 2000-01-22	Different construct Different mutation/modification Different oligomeric state 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 23–104（82 aa）	Mutation：F7A, V13M, F34Y, E43Y, V78I	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	SOLUTION NMR NMR measurement conditions pH 5；298 K；Pressure 1 NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) reduced with dithionite \| 90% H2O/10% D2O NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) reduced with dithionite \| 100% D2O NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) U-15N reduced with dithionite \| 90% H2O/10% D2O NMR sample composition 1mM cytochrome c551(F7A/V13M/F34Y/E43Y/V78I) U-15N,13C reduced with dithionite \| 90% H2O/10% D2O	Resolution not provided
2EXV Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa Deposited 2005-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–104（82 aa）	Mutation：F7A	HEC HEME C × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；294 K；26-30% PEG 4K, zinc acetate 0.2 M, sodium acetate 0.1 M, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.86 Å R-free 0.233
2EXV Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa Deposited 2005-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 23–104（82 aa）	Mutation：F7A	HEC HEME C × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；294 K；26-30% PEG 4K, zinc acetate 0.2 M, sodium acetate 0.1 M, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.86 Å R-free 0.233
2PAC SOLUTION STRUCTURE OF FE(II) CYTOCHROME C551 FROM PSEUDOMONAS AERUGINOSA AS DETERMINED BY TWO-DIMENSIONAL 1H NMR Deposited 1993-05-05	Different construct Different oligomeric state 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 23–104（82 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
351C STRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS Deposited 1981-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–104（82 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
451C STRUCTURE OF CYTOCHROME C551 FROM P. AERUGINOSA REFINED AT 1.6 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO REDOX FORMS Deposited 1981-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–104（82 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
5XEC Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins Deposited 2017-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–42（20 aa） Fragment：UNP RESIDUES 23-42,UNP RESIDUES 37-98 Chain C 43–104（62 aa） Fragment：UNP RESIDUES 19-36,UNP RESIDUES 43-104	Not recorded	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM Tris-HCl containing 200 mM sodium acetate, 30% w/v PEG 4000	Resolution 1.10 Å R-free 0.197
5XED Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins Deposited 2017-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–42（20 aa） Fragment：UNP RESIDUES 23-42,UNP RESIDUES 37-98 Chain C 43–104（62 aa） Fragment：UNP RESIDUES 19-36,UNP RESIDUES 43-104	Mutation：M61A	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM MES containing 25% w/v PEG 6000	Resolution 1.55 Å R-free 0.238

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

View Construct and Data Evidence

UniProt name	CY551_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–82； UniProt 23–104 Author chain B； PDBConstruct 1–82； UniProt 23–104

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	3x39
Deposition date deposition_date	2015-01-16
Structure title title	Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551
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	19.61 Å
Radius of gyration Rg (electron density) rg_electron	18.64 Å
Forward intensity I(0) i0	6565660.00
Molecular weight molecular_weight	18625.0 kDa
Excluded volume excluded_volume	23333 Å³
Envelope volume envelope_volume	31741 Å³
Hydration-shell volume shell_volume	15130 Å³
Envelope diameter envelope_diameter	63.9 Å
Shell Rg shell_rg	23.67 Å
Envelope Rg envelope_rg	18.15 Å
Shape Rg shape_rg	18.63 Å
Total Rg total_rg	19.60 Å
Total atoms total_atoms	1306
Residues n_residues	164
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	64.2 Å
Rg (real space) rg_real	19.49 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	6.5660e+06
I(0) uncertainty (real space) i0_real_error	7.7560e+04
Rg (reciprocal space) rg_reciprocal	19.51 Å
I(0) (reciprocal space) i0_reciprocal	6566000.0000
Solution quality estimate total_estimate	0.8155
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.082
Kurtosis Kurtosis kurtosis	-0.425
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	548700.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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 c-551
Molecular weight formula_weight	8704.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1513

EDPEVLFKNKGCVACHAIDTKMVGPAYKDVAAKFAGQAGAEAELAQRIKNGSQGVWGPIPMPPNAVSDDEAQTLAKWVLSQK

来源 Source

来源生物 organism	Pseudomonas aeruginosa PAO1
NCBI Class编号 ncbi_taxonomy_id	208964
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3x39a_
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	d3x39b_
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 (2 domains)

Domain ID domain_id	3x39A00
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	3x39B00
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	82.611 Å
Unit-cell length b length_b	82.611 Å
Unit-cell length c length_c	89.828 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1418
R_work r_work	0.1395
R_free r_free	0.1881

fit	/app/data/saxs_computation/x3/3x39/3x39.fit
pddf	/app/data/pr_computation/x3/3x39/3x39.pr.out
profile	/app/data/saxs_computation/x3/3x39/3x39.dat

Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551

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

Cytochrome c-551

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