SAXSdb — 3vym

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

Cytochrome c-552

Hydrogenobacter thermophilus

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 19–98	Not recorded	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；100mM HEPES buffer, 800mM ammonium sulfate, 45% (v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.00 Å R-free 0.264

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 3VYM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AYG SOLUTION STRUCTURE OF CYTOCHROME C-552, NMR, 20 STRUCTURES Deposited 1997-11-04	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 19–98（80 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 4.8；298 K；Ionic strength (raw mmCIF value) 120mM ACETATE；Pressure 1 NMR sample composition 90% H2O/10% D2O, OR 99.98% D2O CONTAINING 120MM DEUTERATED ACETATE BUFFER	Resolution not provided
1YNR Crystal structure of the cytochrome c-552 from Hydrogenobacter thermophilus at 2.0 resolution Deposited 2005-01-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 19–98（80 aa） Chain B 19–98（80 aa） Chain C 19–98（80 aa） Chain D 19–98（80 aa）	Not recorded	SO4 SULFATE ION × 3 HEC HEME C × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；MPD, ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.218
2AI5 Solution Structure of Cytochrome C552, determined by Distributed Computing Implementation for NMR data Deposited 2005-07-29	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 19–98（80 aa）	Not recorded	HEC HEME C × 1	SOLUTION NMR NMR measurement conditions pH 4.8；298 K；Ionic strength (raw mmCIF value) 120mM ACETATE BUFFER；Pressure 1 NMR sample composition 2mM CYTOCHROME C-552 \| 90% H2O/10% D2O	Resolution not provided
4ZID Dimeric Hydrogenobacter thermophilus cytochrome c552 obtained from Escherichia coli Deposited 2015-04-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–98（80 aa） Fragment：UNP residues 19-98	Not recorded	HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.6 M sodium citrate buffer	Resolution 1.80 Å R-free 0.203
5AUR Hydrogenobacter thermophilus cytochrome c552 dimer formed by domain swapping at N-terminal region Deposited 2015-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–98（80 aa） Chain C 19–98（80 aa）	Not recorded	HEC HEME C × 2 IOD IODIDE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM potassium iodide, 15% (w/v) PEG 3350	Resolution 1.26 Å R-free 0.229
5AUR Hydrogenobacter thermophilus cytochrome c552 dimer formed by domain swapping at N-terminal region Deposited 2015-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 19–98（80 aa） Chain G 19–98（80 aa）	Not recorded	HEC HEME C × 2 IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；200 mM potassium iodide, 15% (w/v) PEG 3350	Resolution 1.26 Å R-free 0.229
5AUS Hydrogenobacter thermophilus cytochrome c552 dimer formed by domain swapping at C-terminal region Deposited 2015-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–98（80 aa） Chain C 19–98（80 aa）	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, 200 mM sodium acetate, 30% w/v PEG 4000	Resolution 1.30 Å R-free 0.202
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 37–98（62 aa） Fragment：UNP RESIDUES 23-42,UNP RESIDUES 37-98 Chain C 19–36（18 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 37–98（62 aa） Fragment：UNP RESIDUES 23-42,UNP RESIDUES 37-98 Chain C 19–36（18 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

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CY552_HYDTT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–80； UniProt 19–98

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	3vym
Deposition date deposition_date	2012-09-28
Structure title title	Dimeric Hydrogenobacter thermophilus cytochrome c552
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	17.71 Å
Radius of gyration Rg (electron density) rg_electron	17.07 Å
Forward intensity I(0) i0	1752320.00
Molecular weight molecular_weight	9197.0 kDa
Excluded volume excluded_volume	11647 Å³
Envelope volume envelope_volume	15849 Å³
Hydration-shell volume shell_volume	9221 Å³
Envelope diameter envelope_diameter	58.5 Å
Shell Rg shell_rg	20.38 Å
Envelope Rg envelope_rg	16.93 Å
Shape Rg shape_rg	16.98 Å
Total Rg total_rg	18.09 Å
Total atoms total_atoms	644
Residues n_residues	80
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	59.6 Å
Rg (real space) rg_real	17.90 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.7520e+06
I(0) uncertainty (real space) i0_real_error	2.2980e+04
Rg (reciprocal space) rg_reciprocal	17.88 Å
I(0) (reciprocal space) i0_reciprocal	1752000.0000
Solution quality estimate total_estimate	0.7709
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.5 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	154400.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.709; 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-552
Molecular weight formula_weight	8586.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	681

NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK

来源 Source

来源生物 organism	Hydrogenobacter thermophilus
NCBI Class编号 ncbi_taxonomy_id	608538
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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3vyma_
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	3vymA00
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	46.148 Å
Unit-cell length b length_b	46.148 Å
Unit-cell length c length_c	78.407 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	39.970 Å
R factor r_factor	0.2067
R_work r_work	0.2040
R_free r_free	0.2635

fit	/app/data/saxs_computation/vy/3vym/3vym.fit
pddf	/app/data/pr_computation/vy/3vym/3vym.pr.out
profile	/app/data/saxs_computation/vy/3vym/3vym.dat

Dimeric Hydrogenobacter thermophilus cytochrome c552

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

Cytochrome c-552

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