SAXSdb — 2ftx

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

Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 133–221	Fragment：Spc25p globular domain Non-standard monomer：Yes (specific site not provided by mmCIF)	Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region × 1 （Q04477） NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 10.5；293 K；0.1 M CAPS, pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 10.50	Resolution 1.90 Å R-free 0.226

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 2FTX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FV4 NMR solution structure of the yeast kinetochore Spc24/Spc25 globular domain Deposited 2006-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 128–221（94 aa） Fragment：SPC25P GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate buffer；Pressure ambient NMR sample composition 1.5 mM spc25G U-15N,13C,85%-2H, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C,85%-2H, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 85%-2H, 1.5 mM spc24G natural abundance isotopes, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.	Resolution not provided
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 133–221（89 aa） Fragment：Spc25p C-terminal domain, residues 133-221	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293.15 K；15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.01 Å R-free 0.258
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 133–221（89 aa） Fragment：Spc25p C-terminal domain, residues 133-221	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293.15 K；15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.01 Å R-free 0.258
5T6J Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly Deposited 2016-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 133–221（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES, pH 7.0-7.5, 1.0 M potassium sodium tartrate, 0.2 M lithium sulfate	Resolution 1.75 Å R-free 0.242
5TCS Crystal structure of a Dwarf Ndc80 Tetramer Deposited 2016-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–31（31 aa） Chain D 138–221（84 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；1.2 magnesium sulfate, 0.1 M ME pH 6.0	Resolution 2.83 Å R-free 0.266
5TD8 Crystal structure of an Extended Dwarf Ndc80 Complex Deposited 2016-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–45（45 aa） Chain D 138–221（84 aa）	Not recorded	HG MERCURY (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 4,000, 0.1 M CHES, pH 9.0	Resolution 7.53 Å R-free 0.328
8V10 Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–31（31 aa） Chain D 138–221（84 aa）	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；13% polyethylene glycol 8000, 1M sodium chloride 100 mM PIPES pH 6.1	Resolution 3.02 Å R-free 0.271
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–31（31 aa） Chain D 138–220（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–31（31 aa） Chain H 138–220（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
9S4Q Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 25 1–221（221 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
9S5N Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 25 1–221（221 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YEK8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 133–221

Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region

Saccharomyces cerevisiae

UniProt Q04477

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 154–213	Fragment：Spc24p globular domain Non-standard monomer：Yes (specific site not provided by mmCIF)	Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region × 1 （P40014） NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 10.5；293 K；0.1 M CAPS, pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 10.50	Resolution 1.90 Å R-free 0.226

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 2FTX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FV4 NMR solution structure of the yeast kinetochore Spc24/Spc25 globular domain Deposited 2006-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 138–213（76 aa） Fragment：SPC24P GLOBULAR DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate buffer；Pressure ambient NMR sample composition 1.5 mM spc25G U-15N,13C,85%-2H, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C,85%-2H, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G U-15N,13C, 85%-2H, 1.5 mM spc24G natural abundance isotopes, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O. NMR sample composition 1.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O \| 50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.	Resolution not provided
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 155–213（59 aa） Fragment：Spc24p C-terminal domain, residues 155-213	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293.15 K；15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.01 Å R-free 0.258
4GEQ Crystal structure of the Spc24-Spc25/Cnn1 binding interface Deposited 2012-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 155–213（59 aa） Fragment：Spc24p C-terminal domain, residues 155-213	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293.15 K；15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 2.01 Å R-free 0.258
5T6J Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly Deposited 2016-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 155–213（59 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES, pH 7.0-7.5, 1.0 M potassium sodium tartrate, 0.2 M lithium sulfate	Resolution 1.75 Å R-free 0.242
5TCS Crystal structure of a Dwarf Ndc80 Tetramer Deposited 2016-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–48（48 aa） Chain C 162–213（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；1.2 magnesium sulfate, 0.1 M ME pH 6.0	Resolution 2.83 Å R-free 0.266
5TD8 Crystal structure of an Extended Dwarf Ndc80 Complex Deposited 2016-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–62（62 aa） Chain C 162–213（52 aa）	Not recorded	HG MERCURY (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 4,000, 0.1 M CHES, pH 9.0	Resolution 7.53 Å R-free 0.328
8V10 Structure of a Saccharomyces cerevisiae Mps1 peptide bound to dwarf Ndc80 Complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–48（48 aa） Chain C 162–213（52 aa）	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；13% polyethylene glycol 8000, 1M sodium chloride 100 mM PIPES pH 6.1	Resolution 3.02 Å R-free 0.271
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–48（48 aa） Chain C 162–212（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
8V11 Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex Deposited 2023-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–48（48 aa） Chain G 162–212（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291.15 K；15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5	Resolution 3.95 Å R-free 0.327
9S4Q Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 24 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
9S5N Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain Deposited 2025-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain 24 1–213（213 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YM06_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–64； UniProt 154–213

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	2ftx
Deposition date deposition_date	2006-01-25
Structure title title	Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain
Keywords keywords	alpha-beta, complex, coiled-coil, structural protein, protein binding; structural protein, 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	16.94 Å
Radius of gyration Rg (electron density) rg_electron	15.37 Å
Forward intensity I(0) i0	5731520.00
Molecular weight molecular_weight	17032.0 kDa
Excluded volume excluded_volume	21226 Å³
Envelope volume envelope_volume	24699 Å³
Hydration-shell volume shell_volume	13703 Å³
Envelope diameter envelope_diameter	52.7 Å
Shell Rg shell_rg	21.04 Å
Envelope Rg envelope_rg	15.65 Å
Shape Rg shape_rg	15.37 Å
Total Rg total_rg	16.46 Å
Total atoms total_atoms	1188
Residues n_residues	146
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	54.6 Å
Rg (real space) rg_real	16.85 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	5.7320e+06
I(0) uncertainty (real space) i0_real_error	6.5070e+04
Rg (reciprocal space) rg_reciprocal	16.86 Å
I(0) (reciprocal space) i0_reciprocal	5732000.0000
Solution quality estimate total_estimate	0.8904
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.149
Kurtosis Kurtosis kurtosis	-0.379
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	769000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region
Molecular weight formula_weight	10030.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1267

MNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

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 polymer

Description description	Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region
Molecular weight formula_weight	7532.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMEANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

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 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	79

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ftxa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.300 — Kinetochore globular domain-like
Superfamily Superfamily superfamily	d.300.1 — Kinetochore globular domain
Family Family family	d.300.1.1 — Spc25-like

Domain ID domain_id	d2ftxb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.300 — Kinetochore globular domain-like
Superfamily Superfamily superfamily	d.300.1 — Kinetochore globular domain
Family Family family	d.300.1.2 — Spc24-like

CATH v4.4 (2 domains)

Domain ID domain_id	2ftxA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily	50 — Chromosome segregation protein Spc25

Domain ID domain_id	2ftxB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	430 —

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8. Citations (1)

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Unit-cell length a length_a	84.907 Å
Unit-cell length b length_b	84.907 Å
Unit-cell length c length_c	93.195 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	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2100
R_work r_work	0.2090
R_free r_free	0.2260

fit	/app/data/saxs_computation/ft/2ftx/2ftx.fit
pddf	/app/data/pr_computation/ft/2ftx/2ftx.pr.out
profile	/app/data/saxs_computation/ft/2ftx/2ftx.dat

Crystal structure of the yeast kinetochore Spc24/Spc25 globular domain

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

Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region

State in the Current Structure

Other States of the Same Protein in the Database

Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)