SAXSdb — 3bip

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

FACT complex subunit SPT16

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–465	Fragment：residues 1-465	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；298 K；25% Pentaerythritol Ethoxylate (15/4 EO/OH), 100mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.94 Å R-free 0.244
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–465	Fragment：residues 1-465	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.5；298 K；25% Pentaerythritol Ethoxylate (15/4 EO/OH), 100mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, temperature 298K	Resolution 1.94 Å R-free 0.244

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 3BIP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3BIQ Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–465（465 aa） Fragment：residues 1-465	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；25% Pentaerythritol Ethoxylate (15/4 EO/OH), 100mM Sodium Acetate, pH 4.5, vapor diffusion, temperature 298K	Resolution 1.73 Å R-free 0.213
3BIT Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–451（451 aa） Fragment：residues 1-451	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；278 K；35% PEG 300, 200mM NaCl, 100mM Sodium Acetate, pH 4.5, vapor diffusion, temperature 278K	Resolution 1.90 Å R-free 0.224
3BIT Crystal structure of yeast Spt16 N-terminal Domain Deposited 2007-11-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–451（451 aa） Fragment：residues 1-451	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2 BME BETA-MERCAPTOETHANOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；278 K；35% PEG 300, 200mM NaCl, 100mM Sodium Acetate, pH 4.5, vapor diffusion, temperature 278K	Resolution 1.90 Å R-free 0.224
4IOY Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT Deposited 2013-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 675–958（284 aa） Fragment：Middle Domain (UNP residues 675-958)	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；0.1 M sodium/potassium phosphate, pH 6.0, 0.2 M sodium chloride, 40% PEG400, 10 mM TCEP-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.95 Å R-free 0.197
7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric	Chain Q 1–1035（1035 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8XGC Structure of yeast replisome associated with FACT and histone hexamer, Composite map Deposited 2023-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain L 1–1035（1035 aa）	Not recorded	ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	SPT16_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–467； UniProt 1–465 Author chain B； PDBConstruct 3–467； UniProt 1–465

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	3bip
Deposition date deposition_date	2007-11-30
Structure title title	Crystal structure of yeast Spt16 N-terminal Domain
Keywords keywords	;pita-bread, aminopeptidase, chromatin, replication, FACT, Activator, Chromosomal protein, Coiled coil, DNA damage, DNA repair, DNA replication, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription regulation ;; 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	33.62 Å
Radius of gyration Rg (electron density) rg_electron	32.86 Å
Forward intensity I(0) i0	149151000.00
Molecular weight molecular_weight	101240.0 kDa
Excluded volume excluded_volume	128200 Å³
Envelope volume envelope_volume	159610 Å³
Hydration-shell volume shell_volume	40708 Å³
Envelope diameter envelope_diameter	114.3 Å
Shell Rg shell_rg	39.30 Å
Envelope Rg envelope_rg	32.74 Å
Shape Rg shape_rg	32.84 Å
Total Rg total_rg	33.46 Å
Total atoms total_atoms	7150
Residues n_residues	886
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	107.5 Å
Rg (real space) rg_real	33.59 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	1.4920e+08
I(0) uncertainty (real space) i0_real_error	2.4520e+06
Rg (reciprocal space) rg_reciprocal	33.61 Å
I(0) (reciprocal space) i0_reciprocal	149200000.0000
Solution quality estimate total_estimate	0.9023
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	105.2 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46500000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.920

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	FACT complex subunit SPT16
Molecular weight formula_weight	53414.3 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	8034

GHMEELNIDFDVFKKRIELLYSKYNEFEGSPNSLLFVLGSSNAENPYQKTTILHNWLLSYEFPATLIALVPGKVIIITSSAKAKHLQKAIDLFKDPESKITLELWQRNNKEPELNKKLFDDVIALINSAGKTVGIPEKDSYQGKFMTEWNPVWEAAVKENEFNVIDISLGLSKVWEVKDVNEQAFLSVSSKGSDKFMDLLSNEMVRAVDEELKITNAKLSDKIENKIDDVKFLKQLSPDLSALCPPNYKFNFDLLDWTYSPIIQSGKKFDLRVSARSTNDQLYGNGCILASCGIRYNNYCSNITRTFLIDPSEEMANNYDFLLTLQKEIVTNILKPGRTPKEVYESVIEYIEKTKPELVPNFTKNIGSLIGLEFRDSNFILNVKNDYRKIQRGDCFNISFGFNNLKDSQSANNYALQLADTVQIPLDETEPPRFLTNYTKAKSQISFYFNNEEEDNNKKKSSPATKV

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	721

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3bipA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	3bipA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	3bipB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	3bipB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

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8. Citations (1)

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Unit-cell length a length_a	51.142 Å
Unit-cell length b length_b	60.141 Å
Unit-cell length c length_c	85.931 Å
Unit-cell angle α angle_alpha	72.59 °
Unit-cell angle β angle_beta	77.06 °
Unit-cell angle γ angle_gamma	89.88 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	38.910 Å
R factor r_factor	0.1800
R_work r_work	0.1760
R_free r_free	0.2440

fit	/app/data/saxs_computation/bi/3bip/3bip.fit
pddf	/app/data/pr_computation/bi/3bip/3bip.pr.out
profile	/app/data/saxs_computation/bi/3bip/3bip.dat

Crystal structure of yeast Spt16 N-terminal Domain

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

FACT complex subunit SPT16

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