SAXSdb — 2exv

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

Cytochrome c-551

Pseudomonas aeruginosa

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 23–104	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 23–104	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

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 2EXV	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 mutation/modification 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
2PAC SOLUTION STRUCTURE OF FE(II) CYTOCHROME C551 FROM PSEUDOMONAS AERUGINOSA AS DETERMINED BY TWO-DIMENSIONAL 1H NMR Deposited 1993-05-05	Different mutation/modification 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 mutation/modification 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
3X39 Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551 Deposited 2015-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–104（82 aa） Fragment：UNP residues 23-104	Not recorded	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
3X39 Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551 Deposited 2015-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 23–104（82 aa） Fragment：UNP residues 23-104	Not recorded	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
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 mutation/modification 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 ligand/ion 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 ligand/ion 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 C； 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	2exv
Deposition date deposition_date	2005-11-09
Structure title title	Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa
Keywords keywords	cytochrome c, alpha helix, heme c, 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	18.22 Å
Radius of gyration Rg (electron density) rg_electron	17.50 Å
Forward intensity I(0) i0	6347190.00
Molecular weight molecular_weight	18465.0 kDa
Excluded volume excluded_volume	23095 Å³
Envelope volume envelope_volume	26660 Å³
Hydration-shell volume shell_volume	13411 Å³
Envelope diameter envelope_diameter	61.9 Å
Shell Rg shell_rg	22.39 Å
Envelope Rg envelope_rg	17.88 Å
Shape Rg shape_rg	17.49 Å
Total Rg total_rg	18.32 Å
Total atoms total_atoms	1293
Residues n_residues	163
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	61.9 Å
Rg (real space) rg_real	18.28 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	6.3470e+06
I(0) uncertainty (real space) i0_real_error	7.8040e+04
Rg (reciprocal space) rg_reciprocal	18.27 Å
I(0) (reciprocal space) i0_reciprocal	6347000.0000
Solution quality estimate total_estimate	0.8455
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.412
Kurtosis Kurtosis kurtosis	-0.433
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3617000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.986

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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-551
Molecular weight formula_weight	8628.8 kDa
Mutation mutation	F7A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1463

EDPEVLAKNKGCVACHAIDTKMVGPAYKDVAAKFAGQAGAEAELAQRIKNGSQGVWGPIPMPPNAVSDDEAQTLAKWVLSQK

来源 Source

来源生物 organism	Pseudomonas aeruginosa
NCBI Class编号 ncbi_taxonomy_id	287
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 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 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	128

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2exva_
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	d2exvc_
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	2exvA00
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	2exvC00
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 (4)

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Unit-cell length a length_a	66.766 Å
Unit-cell length b length_b	66.766 Å
Unit-cell length c length_c	62.462 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	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1782
R_work r_work	0.1754
R_free r_free	0.2329

fit	/app/data/saxs_computation/ex/2exv/2exv.fit
pddf	/app/data/pr_computation/ex/2exv/2exv.pr.out
profile	/app/data/saxs_computation/ex/2exv/2exv.dat

Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa

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