SAXSdb — 2fvu

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

Regulatory protein SIR3

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 1–218 Chain B； UniProt 1–218	Fragment：BAH domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.75；290 K；4M sodium formate, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.308

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 2FVU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FL7 S. cerevisiae Sir3 BAH domain Deposited 2006-01-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–228（228 aa） Fragment：BAH domain, residues 1-229	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M HEPES, pH 6.5, 200 mM sodium chloride, 10% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.232
3OWT Crystal structure of S. cerevisiae RAP1-Sir3 complex Deposited 2010-09-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 456–481（26 aa） Fragment：Rap1-interaction motif (UNP residues 456 to 481)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；100 mM sodium citrate pH 4.8, 30% PEG4K, 200 mM ammonium acetate, and 10 mM DTT , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.260
3TE6 Crystal Structure of the S. cerevisiae Sir3 AAA+ domain Deposited 2011-08-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 530–845（316 aa） Fragment：AAA+ domain (UNP Residues 530-845)	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 7.5；277 K；2 M ammonium sulfate, 2% (w/v) PEG 400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.276
3TE6 Crystal Structure of the S. cerevisiae Sir3 AAA+ domain Deposited 2011-08-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 530–845（316 aa） Fragment：AAA+ domain (UNP Residues 530-845)	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 7.5；277 K；2 M ammonium sulfate, 2% (w/v) PEG 400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.276
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 1–213（213 aa） Fragment：BAH domain Chain L 1–213（213 aa） Fragment：BAH domain	Mutation：D205N Mutation：D205N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.241
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 1–213（213 aa） Fragment：BAH domain	Mutation：D205N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.241
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 1–213（213 aa） Fragment：BAH domain	Mutation：D205N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.00 Å R-free 0.241
3ZCO Crystal structure of S. cerevisiae Sir3 C-terminal domain Deposited 2012-11-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 840–978（139 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 840-978	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 30% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE PH 5.6	Resolution 2.70 Å R-free 0.263
4JJN Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome Deposited 2013-03-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 2–382（381 aa） Chain L 2–382（381 aa）	Mutation：D205N Mutation：D205N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.09 Å R-free 0.255
4KUD Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle Deposited 2013-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 2–219（218 aa） Fragment：BAH domain, UNP residues 2-219 Chain L 2–219（218 aa） Fragment：BAH domain, UNP residues 2-219	Mutation：D205N Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D205N 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 4.8；289 K；16% PEG 400, 0.1M KCl, 0.01M CaCl2, 0.05M sodium citrate(pH4.8), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.20 Å R-free 0.237
4KUI Crystal structure of N-terminal acetylated yeast Sir3 BAH domain Deposited 2013-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–219（218 aa） Fragment：BAH domain, UNP residues 2-219	Non-standard monomer：Yes (specific site not provided by mmCIF)	IPA ISOPROPYL ALCOHOL × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；289 K；18% 2-propanol, 0.2M CaCl, 0.1M sodium acetate (pH4.6), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.85 Å R-free 0.199
4KUL Crystal structure of N-terminal acetylated yeast Sir3 BAH domain V83P mutant Deposited 2013-05-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–219（218 aa） Fragment：BAH domain, UNP residues 2-219	Mutation：V83P 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 4.6；289 K；14% 2-propanol, 0.2M CaCl, 0.1M sodium acetate(pH4.6) , VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.62 Å R-free 0.277
4LD9 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Deposited 2013-06-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 2–229（228 aa） Chain L 2–229（228 aa）	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；pH 6.5；293.15 K；50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K	Resolution 3.31 Å R-free 0.295

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

View Construct and Data Evidence

UniProt name	SIR3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–222； UniProt 1–218 Author chain B； PDBConstruct 4–222； UniProt 1–218

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	2fvu
Deposition date deposition_date	2006-01-31
Structure title title	Structure of the yeast Sir3 BAH domain
Keywords keywords	mainly beta, TRANSCRIPTION; TRANSCRIPTION
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	26.41 Å
Radius of gyration Rg (electron density) rg_electron	25.97 Å
Forward intensity I(0) i0	30760200.00
Molecular weight molecular_weight	45576.0 kDa
Excluded volume excluded_volume	58071 Å³
Envelope volume envelope_volume	71458 Å³
Hydration-shell volume shell_volume	24669 Å³
Envelope diameter envelope_diameter	108.5 Å
Shell Rg shell_rg	31.15 Å
Envelope Rg envelope_rg	26.23 Å
Shape Rg shape_rg	26.00 Å
Total Rg total_rg	26.48 Å
Total atoms total_atoms	3229
Residues n_residues	381
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	104.6 Å
Rg (real space) rg_real	26.67 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	3.0760e+07
I(0) uncertainty (real space) i0_real_error	4.6790e+05
Rg (reciprocal space) rg_reciprocal	26.59 Å
I(0) (reciprocal space) i0_reciprocal	30760000.0000
Solution quality estimate total_estimate	0.7573
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.695
Kurtosis Kurtosis kurtosis	0.386
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5079000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.438; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.537; Smooth: 0.991

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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) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2fvua1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.12 — BAH domain
Family Family family	b.34.12.0 — automated matches

Domain ID domain_id	d2fvua2
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	d2fvub1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.12 — BAH domain
Family Family family	b.34.12.0 — automated matches

Domain ID domain_id	d2fvub2
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 (2 domains)

Domain ID domain_id	2fvuA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	490 — Bromo adjacent homology (BAH) domain

Domain ID domain_id	2fvuB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	490 — Bromo adjacent homology (BAH) domain

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8. Citations (1)

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Unit-cell length a length_a	130.390 Å
Unit-cell length b length_b	130.390 Å
Unit-cell length c length_c	65.590 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 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	500.000 Å
R factor r_factor	0.2800
R_work r_work	0.2800
R_free r_free	0.3080

Description description	Regulatory protein SIR3
Molecular weight formula_weight	26405.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3353

Structure of the yeast Sir3 BAH domain

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

Regulatory protein SIR3

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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 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	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

fit	/app/data/saxs_computation/fv/2fvu/2fvu.fit
pddf	/app/data/pr_computation/fv/2fvu/2fvu.pr.out
profile	/app/data/saxs_computation/fv/2fvu/2fvu.dat