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3bit

Crystal structure of yeast Spt16 N-terminal Domain

Method: X-RAY DIFFRACTION Dmax: 104.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

FACT complex subunit SPT16

Saccharomyces cerevisiae

UniProt P32558

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 1–451 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–451 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

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 3BIT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BIP 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 1–465（465 aa） Fragment：residues 1-465
Not recorded No recorded non-water small molecule 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
3BIP 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 1–465（465 aa） Fragment：residues 1-465
Not recorded No recorded non-water small molecule 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
3BIQ 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 1–465（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
4IOY Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT Deposited 2013-01-08 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 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 mutation/modification 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 mutation/modification 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 3–453； UniProt 1–451 Author chain B； PDBConstruct 3–453； UniProt 1–451

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3bit

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3bit
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3bit
Deposition date deposition_date2007-11-30
Structure title titleCrystal structure of yeast Spt16 N-terminal Domain
Keywords keywords;pita-bread, aminopeptidase, chromatin, replication, FACT, Activator, Chromosomal protein, DNA damage, DNA repair, DNA replication, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription regulation ;; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.03 Å
Radius of gyration Rg (electron density) rg_electron32.61 Å
Forward intensity I(0) i0153879000.00
Molecular weight molecular_weight102070.0 kDa
Excluded volume excluded_volume128750 ų
Envelope volume envelope_volume161620 ų
Hydration-shell volume shell_volume41178 ų
Envelope diameter envelope_diameter112.5 Å
Shell Rg shell_rg39.56 Å
Envelope Rg envelope_rg32.35 Å
Shape Rg shape_rg32.63 Å
Total Rg total_rg33.08 Å
Total atoms total_atoms7166
Residues n_residues876
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.0 Å
Rg (real space) rg_real32.98 Å
Rg uncertainty (real space) rg_real_error0.78 Å
I(0) (real space) i0_real1.5390e+08
I(0) uncertainty (real space) i0_real_error2.2890e+06
Rg (reciprocal space) rg_reciprocal33.00 Å
I(0) (reciprocal space) i0_reciprocal153900000.0000
Solution quality estimate total_estimate0.8987
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.0 Å
Skewness Skewness skewness0.250
Kurtosis Kurtosis kurtosis-0.518
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha55960000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.830
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3bitA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Creatinase/prolidase N-terminal domain
Domain ID domain_id3bitA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily10 — Creatinase/methionine aminopeptidase superfamily
Domain ID domain_id3bitB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Creatinase/prolidase N-terminal domain
Domain ID domain_id3bitB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily10 — Creatinase/methionine aminopeptidase superfamily
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8. Citations (1)

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9. Files and Curves (10)