SAXSdb — 2doq

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

Cell division control protein 31

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–161 Chain B； UniProt 1–161 Chain C； UniProt 1–161	Non-standard monomer：Yes (specific site not provided by mmCIF)	SFI1p × 1 （Q12369） CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；9% iso-propanol, 0.1M MES pH=6.2, 0.2M Ca(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299

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 2DOQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GV5 crystal structure of Sfi1p/Cdc31p complex Deposited 2006-05-02	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 1–161（161 aa） Chain B 1–161（161 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, SITTING DROP；pH 8.5；277 K；0.2 M sodium acetate, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.297
2GV5 crystal structure of Sfi1p/Cdc31p complex Deposited 2006-05-02	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 1–161（161 aa） Chain E 1–161（161 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, SITTING DROP；pH 8.5；277 K；0.2 M sodium acetate, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.297
3FWB Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–161（161 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1M MES pH6.5, 16% PEG4K, 20% glycerol - see publication for complete details, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.235
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–161（161 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–161（161 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–161（161 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
3FWC Sac3:Sus1:Cdc31 complex Deposited 2009-01-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 1–161（161 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；unbuffered 16% PEG4K, 20% glycerol, 0.2 M Am sulph. See publication for complete details, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.265
4MBE Sac3:Sus1:Cdc31:Nup1 complex Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–161（161 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.61 Å R-free 0.236
4MBE Sac3:Sus1:Cdc31:Nup1 complex Deposited 2013-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–161（161 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.61 Å R-free 0.236

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

View Construct and Data Evidence

UniProt name	CDC31_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–161； UniProt 1–161 Author chain B； PDBConstruct 1–161； UniProt 1–161 Author chain C； PDBConstruct 1–161； UniProt 1–161

SFI1p

Saccharomyces cerevisiae

UniProt Q12369

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 218–306	Fragment：Residues: 218 - 306 Non-standard monomer：Yes (specific site not provided by mmCIF)	Cell division control protein 31 × 3 （P06704） CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.2；277 K；9% iso-propanol, 0.1M MES pH=6.2, 0.2M Ca(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299

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 2DOQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GV5 crystal structure of Sfi1p/Cdc31p complex Deposited 2006-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 643–710（68 aa） Fragment：Residues: 643-710	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, SITTING DROP；pH 8.5；277 K；0.2 M sodium acetate, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.297
2GV5 crystal structure of Sfi1p/Cdc31p complex Deposited 2006-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 643–710（68 aa） Fragment：Residues: 643-710	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, SITTING DROP；pH 8.5；277 K；0.2 M sodium acetate, 18% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.00 Å R-free 0.297

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q12369_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 6–94； UniProt 218–306

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	2doq
Deposition date deposition_date	2006-05-03
Structure title title	crystal structure of Sfi1p/Cdc31p complex
Keywords keywords	Sfi1p, centrin, cdc31p, spindle pole body, centrosome, Cell Cycle; CELL CYCLE
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	38.85 Å
Radius of gyration Rg (electron density) rg_electron	39.91 Å
Forward intensity I(0) i0	60216500.00
Molecular weight molecular_weight	60972.0 kDa
Excluded volume excluded_volume	75440 Å³
Envelope volume envelope_volume	111880 Å³
Hydration-shell volume shell_volume	27080 Å³
Envelope diameter envelope_diameter	139.9 Å
Shell Rg shell_rg	38.17 Å
Envelope Rg envelope_rg	40.26 Å
Shape Rg shape_rg	39.90 Å
Total Rg total_rg	39.84 Å
Total atoms total_atoms	4226
Residues n_residues	491
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	144.8 Å
Rg (real space) rg_real	39.79 Å
Rg uncertainty (real space) rg_real_error	2.11 Å
I(0) (real space) i0_real	6.0220e+07
I(0) uncertainty (real space) i0_real_error	1.1170e+06
Rg (reciprocal space) rg_reciprocal	39.21 Å
I(0) (reciprocal space) i0_reciprocal	60180000.0000
Solution quality estimate total_estimate	0.6962
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.628
Kurtosis Kurtosis kurtosis	-0.425
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3835000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.345; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.149; Smooth: 0.861

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cell division control protein 31
Molecular weight formula_weight	19055.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4230

MSKNRSSLQSGPLNSELLEEQKQEIYEAFSLFDMNNDGFLDYHELKVAMKALGFELPKREILDLIDEYDSEGRHLMKYDDFYIVMGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAMIEEFDLDGDGEINENEFIAICTDS

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	SFI1p
Molecular weight formula_weight	11397.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GPLGSNEEANRFANQAKLRVQEAVFYIWSDKTLKYSQMANDEAESFRNTWLLFRSFQQWITLTQTFKEQSRLADQAFLNKMFRKILKAQEHWKH

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2doqa_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

Domain ID domain_id	d2doqb_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

Domain ID domain_id	d2doqc_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	2doqA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2doqB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2doqB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2doqC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2doqD00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1000 —

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8. Citations (1)

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Unit-cell length a length_a	87.283 Å
Unit-cell length b length_b	92.961 Å
Unit-cell length c length_c	189.358 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	94.490 Å
R factor r_factor	0.2606
R_work r_work	0.2586
R_free r_free	0.2990

fit	/app/data/saxs_computation/do/2doq/2doq.fit
pddf	/app/data/pr_computation/do/2doq/2doq.pr.out
profile	/app/data/saxs_computation/do/2doq/2doq.dat

crystal structure of Sfi1p/Cdc31p complex

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

Cell division control protein 31

State in the Current Structure

Other States of the Same Protein in the Database

SFI1p

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 (4)

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 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)