SAXSdb — 2xfv

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

REGULATORY PROTEIN SWI6

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 2–126 Chain B； UniProt 2–126	Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 2-126	CA CALCIUM ION × 3 GOL GLYCEROL × 3 ACT ACETATE ION × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；5-15MG/ML PROTEIN, 10% PEG4000, 0.1M NA-CACODYLATE, 20MM CA-ACETATE, 0.2M NH4CL, PH 6.5	Resolution 1.90 Å R-free 0.196

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 2XFV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SW6 S. CEREVISIAE SWI6 ANKYRIN-REPEAT FRAGMENT Deposited 1998-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 188–512（325 aa） Fragment：ANKYRIN-REPEAT DOMAIN Chain B 188–512（325 aa） Fragment：ANKYRIN-REPEAT DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.50	Resolution 2.10 Å R-free 0.251
5XW5 Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide Deposited 2017-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 155–164（10 aa） Fragment：UNP residues 155-164	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 6；293 K；Bis-Tris, ammonium sulfate, PEG 4000	Resolution 1.85 Å R-free 0.217

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

View Construct and Data Evidence

UniProt name	SWI6_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–125； UniProt 2–126 Author chain B； PDBConstruct 1–125； UniProt 2–126

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	2xfv
Deposition date deposition_date	2010-05-27
Structure title title	Structure of the amino-terminal domain from the cell-cycle regulator Swi6
Keywords keywords	CELL-CYCLE, REGULATION, CELL CYCLE; CELL CYCLE
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	21.00 Å
Radius of gyration Rg (electron density) rg_electron	19.64 Å
Forward intensity I(0) i0	11699900.00
Molecular weight molecular_weight	25640.0 kDa
Excluded volume excluded_volume	32018 Å³
Envelope volume envelope_volume	38999 Å³
Hydration-shell volume shell_volume	17198 Å³
Envelope diameter envelope_diameter	68.8 Å
Shell Rg shell_rg	25.13 Å
Envelope Rg envelope_rg	19.78 Å
Shape Rg shape_rg	19.62 Å
Total Rg total_rg	20.51 Å
Total atoms total_atoms	1804
Residues n_residues	216
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	66.8 Å
Rg (real space) rg_real	20.98 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.1700e+07
I(0) uncertainty (real space) i0_real_error	1.4820e+05
Rg (reciprocal space) rg_reciprocal	20.98 Å
I(0) (reciprocal space) i0_reciprocal	11700000.0000
Solution quality estimate total_estimate	0.8187
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1985000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	REGULATORY PROTEIN SWI6
Molecular weight formula_weight	14519.9 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	2196

ALEEVVRYLGPHNEIPLTLTRDSETGHFLLKHFLPILQQYHDTGNINETNPDSFPTDEERNKLLAHYGIAVNTDDRGELWIELEKCLQLLNMLNLFGLFQDAFEFEEPETDQDEEDPSHSKLPEN

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	329

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2xfvA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	2xfvB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	260 — Mlu1-box Binding Protein; DNA-binding Domain
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	69.934 Å
Unit-cell length b length_b	69.934 Å
Unit-cell length c length_c	297.944 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 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.784 Å
R factor r_factor	0.1717
R_work r_work	0.1705
R_free r_free	0.1962

fit	/app/data/saxs_computation/xf/2xfv/2xfv.fit
pddf	/app/data/pr_computation/xf/2xfv/2xfv.pr.out
profile	/app/data/saxs_computation/xf/2xfv/2xfv.dat

Structure of the amino-terminal domain from the cell-cycle regulator Swi6

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

REGULATORY PROTEIN SWI6

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