SAXSdb — 3okq

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

Bud site selection protein 6

Saccharomyces cerevisiae

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 549–688	Fragment：coiled-coil domain (unp residues 549-688)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；12% PEG 3350, 175 mM sodium malonate (pH 7.0), 20% glycerol, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.04 Å R-free 0.227

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 3OKQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ONX Crystal structure of a domain of a protein involved in formation of actin cytoskeleton Deposited 2010-08-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 549–688（140 aa） Fragment：coiled-coil domain (unp residues 549-688) Chain B 549–688（140 aa） Fragment：coiled-coil domain (unp residues 549-688)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；9% PEG 3350, 85 mM sodium malonate (pH 7.0), 25% glycerol, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.278
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain V 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258
4WYB Structure of the Bud6 flank domain in complex with actin Deposited 2014-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 699–788（90 aa） Fragment：residues 699-788	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；3.5M sodium formate, 0.1M CaCl2, and 5 mM TCEP	Resolution 3.49 Å R-free 0.258

2 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BUD6_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–141； UniProt 549–688

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	3okq
Deposition date deposition_date	2010-08-25
Structure title title	Crystal structure of a core domain of yeast actin nucleation cofactor Bud6
Keywords keywords	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	31.07 Å
Radius of gyration Rg (electron density) rg_electron	33.22 Å
Forward intensity I(0) i0	3749040.00
Molecular weight molecular_weight	14534.0 kDa
Excluded volume excluded_volume	18210 Å³
Envelope volume envelope_volume	27563 Å³
Hydration-shell volume shell_volume	9348 Å³
Envelope diameter envelope_diameter	121.8 Å
Shell Rg shell_rg	29.33 Å
Envelope Rg envelope_rg	34.22 Å
Shape Rg shape_rg	33.08 Å
Total Rg total_rg	33.17 Å
Total atoms total_atoms	1017
Residues n_residues	125
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	125.5 Å
Rg (real space) rg_real	32.33 Å
Rg uncertainty (real space) rg_real_error	2.05 Å
I(0) (real space) i0_real	3.7490e+06
I(0) uncertainty (real space) i0_real_error	7.4330e+04
Rg (reciprocal space) rg_reciprocal	31.79 Å
I(0) (reciprocal space) i0_reciprocal	3747000.0000
Solution quality estimate total_estimate	0.5955
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.787
Kurtosis Kurtosis kurtosis	-0.069
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	154200.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.043; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.002; Smooth: 0.606

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3okqA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1540 — Actin interacting protein 3, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	58.883 Å
Unit-cell length b length_b	95.214 Å
Unit-cell length c length_c	70.787 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.044 Å
Low-resolution limit resolution_low	35.394 Å
R factor r_factor	0.1946
R_work r_work	0.1920
R_free r_free	0.2265

Description description	Bud site selection protein 6
Molecular weight formula_weight	16355.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1144

Crystal structure of a core domain of yeast actin nucleation cofactor Bud6

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

Bud site selection protein 6

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

fit	/app/data/saxs_computation/ok/3okq/3okq.fit
pddf	/app/data/pr_computation/ok/3okq/3okq.pr.out
profile	/app/data/saxs_computation/ok/3okq/3okq.dat