SAXSdb — 2g3k

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

Vacuolar protein sorting-associated protein VPS28

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 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
10	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 148–241 Chain G； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
11	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 148–241 Chain F； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
8	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 148–241 Chain B； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273
9	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 148–241 Chain B； UniProt 148–241 Chain F； UniProt 148–241	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1 M AS 100 mM sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.273

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 2G3K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CAZ ESCRT-I core Deposited 2005-12-23	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 B 1–147（147 aa） Fragment：RESIDUES 1-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2CAZ ESCRT-I core Deposited 2005-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–147（147 aa） Fragment：RESIDUES 1-147	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；290 K；8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C	Resolution 3.60 Å R-free 0.357
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	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 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125)	Mutation：C101A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125)	Mutation：C101A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F66 Structure of the ESCRT-I endosomal trafficking complex Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125) Chain E 13–125（113 aa） Fragment：Vps28N-Terminal Domain (13-125)	Mutation：C101A Mutation：C101A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.256
2F6M Structure of a Vps23-C:Vps28-N subcomplex Deposited 2005-11-29	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 B 13–118（106 aa） Fragment：Vps28N-terminal domain (13-118)	Mutation：C101A	MG MAGNESIUM ION × 1 DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261
2F6M Structure of a Vps23-C:Vps28-N subcomplex Deposited 2005-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 13–118（106 aa） Fragment：Vps28N-terminal domain (13-118)	Mutation：C101A	DDQ DECYLAMINE-N,N-DIMETHYL-N-OXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.261
2J9U 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II Deposited 2006-11-16	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 A 148–242（95 aa） Fragment：RESIDUES 148-242	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% ETHANOL, 0.1M KCL, pH 7.40	Resolution 2.00 Å R-free 0.260
2J9U 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus in complex with the NZF-N domain from ESCRT-II Deposited 2006-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 148–242（95 aa） Fragment：RESIDUES 148-242	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% ETHANOL, 0.1M KCL, pH 7.40	Resolution 2.00 Å R-free 0.260
2J9V 2 Angstrom X-ray structure of the yeast ESCRT-I Vps28 C-terminus Deposited 2006-11-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 148–242（95 aa） Fragment：RESIDUES 148-242	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；4% PEG 400, 0.1M LITHIUM SULPHATE, 0.1M SODIUM CITRATE (PH5.6), pH 5.60	Resolution 2.00 Å R-free 0.255
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	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 B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315
2P22 Structure of the Yeast ESCRT-I Heterotetramer Core Deposited 2007-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–118（118 aa） Fragment：Vps28N-Terminal Domain (1-118)	Mutation：C101A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；294 K；Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.315

6 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS28_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 148–241 Author chain B； PDBConstruct 1–94； UniProt 148–241 Author chain C； PDBConstruct 1–94； UniProt 148–241 Author chain D； PDBConstruct 1–94； UniProt 148–241 Author chain E； PDBConstruct 1–94； UniProt 148–241 Author chain F； PDBConstruct 1–94； UniProt 148–241 Author chain G； PDBConstruct 1–94； UniProt 148–241

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	2g3k
Deposition date deposition_date	2006-02-20
Structure title title	Crystal structure of the C-terminal domain of Vps28
Keywords keywords	4 helix bundle, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	28.11 Å
Radius of gyration Rg (electron density) rg_electron	27.02 Å
Forward intensity I(0) i0	86156300.00
Molecular weight molecular_weight	76577.0 kDa
Excluded volume excluded_volume	97516 Å³
Envelope volume envelope_volume	120010 Å³
Hydration-shell volume shell_volume	36362 Å³
Envelope diameter envelope_diameter	94.8 Å
Shell Rg shell_rg	34.90 Å
Envelope Rg envelope_rg	27.01 Å
Shape Rg shape_rg	27.04 Å
Total Rg total_rg	27.83 Å
Total atoms total_atoms	5390
Residues n_residues	651
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	90.7 Å
Rg (real space) rg_real	27.94 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	8.6160e+07
I(0) uncertainty (real space) i0_real_error	1.2130e+06
Rg (reciprocal space) rg_reciprocal	28.00 Å
I(0) (reciprocal space) i0_reciprocal	86160000.0000
Solution quality estimate total_estimate	0.8923
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.6 Å
Skewness Skewness skewness	0.181
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15490000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.985

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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) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2g3ka1
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2g3kb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2g3kc_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2g3kd_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2g3ke_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2g3kf_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

Domain ID domain_id	d2g3kg_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.28 — VPS28 C-terminal domain-like
Family Family family	a.24.28.1 — VPS28 C-terminal domain-like

CATH v4.4 (7 domains)

Domain ID domain_id	2g3kA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2g3kB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2g3kC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2g3kD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2g3kE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2g3kF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

Domain ID domain_id	2g3kG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1130 — Vps28 C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	117.579 Å
Unit-cell length b length_b	117.579 Å
Unit-cell length c length_c	294.116 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	84

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	19.940 Å
R factor r_factor	0.2160
R_work r_work	0.2130
R_free r_free	0.2727

Description description	Vacuolar protein sorting-associated protein VPS28
Molecular weight formula_weight	10952.4 kDa
Source method src_method	man
Copy count entity_count	7

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	5446

Crystal structure of the C-terminal domain of Vps28

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

Vacuolar protein sorting-associated protein VPS28

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

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) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

fit	/app/data/saxs_computation/g3/2g3k/2g3k.fit
pddf	/app/data/pr_computation/g3/2g3k/2g3k.pr.out
profile	/app/data/saxs_computation/g3/2g3k/2g3k.dat