SAXSdb — 1ybk

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

tetrabrachion

Staphylothermus marinus

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1238–1287 Chain B； UniProt 1238–1287 Chain C； UniProt 1238–1287 Chain D； UniProt 1238–1287	Not recorded	SO4 SULFATE ION × 3 BEQ N-(CARBOXYMETHYL)-N,N-DIMETHYL-3-[(1-OXODODECYL)AMINO]-1-PROPANAMINIUM INNER SALT × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；273 K；ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.45 Å R-free 0.226

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 1YBK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FE6 CRYSTAL STRUCTURE OF A NATURALLY OCCURING PARALLEL RIGHT-HANDED COILED-COIL TETRAMER Deposited 2000-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1238–1286（49 aa） Fragment：RIGHT HANDED COILED COIL Chain B 1238–1286（49 aa） Fragment：RIGHT HANDED COILED COIL Chain C 1238–1286（49 aa） Fragment：RIGHT HANDED COILED COIL Chain D 1238–1286（49 aa） Fragment：RIGHT HANDED COILED COIL	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.216
5JR5 RHCC in Complex with Elemental Sulfur Deposited 2016-05-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain B 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain C 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain D 1238–1287（50 aa） Fragment：UNP residues 1238-1287	Not recorded	PS9 octathiocane × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.6M ammonium sulfate and 100 mM Tris pH 8.0	Resolution 1.90 Å R-free 0.207
5VH0 RHCC in complex with pyrene Deposited 2017-04-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain B 1238–1287（50 aa） Fragment：UNP residues 1238-1287	Not recorded	8P0 pyrene × 4 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG 3350,0.1M Bis-Tris pH 5.5, 200mM NaCl	Resolution 2.06 Å R-free 0.259
5VH0 RHCC in complex with pyrene Deposited 2017-04-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain D 1238–1287（50 aa） Fragment：UNP residues 1238-1287	Not recorded	8P0 pyrene × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；25% PEG 3350,0.1M Bis-Tris pH 5.5, 200mM NaCl	Resolution 2.06 Å R-free 0.259
5VKF RHCC in complex with Naphthalene Deposited 2017-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain B 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain C 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain D 1238–1287（50 aa） Fragment：UNP residues 1238-1287	Not recorded	SO4 SULFATE ION × 3 NPY NAPHTHALENE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277.15 K；1.5M Ammonium Sulfate, 0.1M Tris pH 8.5	Resolution 2.75 Å R-free 0.239
6CRD INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk Deposited 2018-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1251–1285（35 aa） Chain B 1251–1285（35 aa） Chain E 1251–1285（35 aa） Chain H 1251–1285（35 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100 mM HEPES buffer at pH7.0 with 10% PEG6000	Resolution 2.57 Å R-free 0.306
6CRD INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk Deposited 2018-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1251–1285（35 aa） Chain D 1251–1285（35 aa） Chain F 1251–1285（35 aa） Chain G 1251–1285（35 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100 mM HEPES buffer at pH7.0 with 10% PEG6000	Resolution 2.57 Å R-free 0.306
7R6H RHCC in complex with o-carborane Deposited 2021-06-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain B 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain C 1238–1287（50 aa） Fragment：UNP residues 1238-1287 Chain D 1238–1287（50 aa） Fragment：UNP residues 1238-1287	Not recorded	1KW ortho-carborane × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M ammonium acetate, 0.05 M sodium cacodylate trihydrate, 10% v/v 2-propanol, 0.015 M magnesium acetate tetrahydrate	Resolution 2.20 Å R-free 0.266

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

View Construct and Data Evidence

UniProt name	Q54436_STAMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–52； UniProt 1238–1287 Author chain B； PDBConstruct 3–52； UniProt 1238–1287 Author chain C； PDBConstruct 3–52； UniProt 1238–1287 Author chain D； PDBConstruct 3–52； UniProt 1238–1287

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	1ybk
Deposition date deposition_date	2004-12-21
Structure title title	RHCC cocrystallized with CAPB
Keywords keywords	right hand coiled coil, PROTEIN BINDING; PROTEIN BINDING
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	23.08 Å
Radius of gyration Rg (electron density) rg_electron	22.60 Å
Forward intensity I(0) i0	10377000.00
Molecular weight molecular_weight	23549.0 kDa
Excluded volume excluded_volume	29351 Å³
Envelope volume envelope_volume	35461 Å³
Hydration-shell volume shell_volume	15198 Å³
Envelope diameter envelope_diameter	82.7 Å
Shell Rg shell_rg	26.91 Å
Envelope Rg envelope_rg	23.20 Å
Shape Rg shape_rg	22.60 Å
Total Rg total_rg	23.21 Å
Total atoms total_atoms	1646
Residues n_residues	205
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	66.9 Å
Rg (real space) rg_real	21.89 Å
Rg uncertainty (real space) rg_real_error	0.17 Å
I(0) (real space) i0_real	9.9960e+06
I(0) uncertainty (real space) i0_real_error	1.1250e+05
Rg (reciprocal space) rg_reciprocal	23.38 Å
I(0) (reciprocal space) i0_reciprocal	10380000.0000
Solution quality estimate total_estimate	0.6243
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	19.6 Å
Skewness Skewness skewness	0.544
Kurtosis Kurtosis kurtosis	-0.370
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	1.9540
Highest regularization parameter α highest_alpha	6190000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 0.971; Sysdev: 0.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.000

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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	tetrabrachion
Molecular weight formula_weight	5898.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2135

GSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASI

来源 Source

来源生物 organism	Staphylothermus marinus
NCBI Class编号 ncbi_taxonomy_id	2280
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	N-(CARBOXYMETHYL)-N,N-DIMETHYL-3-[(1-OXODODECYL)AMINO]-1-PROPANAMINIUM INNER SALT
Molecular weight formula_weight	342.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	489

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1ybka1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.19 — Tetrabrachion
Family Family family	h.1.19.1 — Tetrabrachion

Domain ID domain_id	d1ybka2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ybkb1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.19 — Tetrabrachion
Family Family family	h.1.19.1 — Tetrabrachion

Domain ID domain_id	d1ybkb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1ybkc_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.19 — Tetrabrachion
Family Family family	h.1.19.1 — Tetrabrachion

Domain ID domain_id	d1ybkd1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.19 — Tetrabrachion
Family Family family	h.1.19.1 — Tetrabrachion

Domain ID domain_id	d1ybkd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	1ybkA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1060 — Tetrabrachion

Domain ID domain_id	1ybkB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1060 — Tetrabrachion

Domain ID domain_id	1ybkC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1060 — Tetrabrachion

Domain ID domain_id	1ybkD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1060 — Tetrabrachion

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8. Citations (1)

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Unit-cell length a length_a	110.811 Å
Unit-cell length b length_b	110.811 Å
Unit-cell length c length_c	71.121 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2260

fit	/app/data/saxs_computation/yb/1ybk/1ybk.fit
pddf	/app/data/pr_computation/yb/1ybk/1ybk.pr.out
profile	/app/data/saxs_computation/yb/1ybk/1ybk.dat

RHCC cocrystallized with CAPB