SAXSdb — 2vpv

▼

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

PROTEIN MIF2

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 365–530 Chain B； UniProt 365–530	Fragment：DIMERIZATION DOMAIN, RESIDUES 365-530	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP VAPOR FUSION FROM 3-4% (W/V) PEG 3000, 100 MM IMIDAZOLE (PH 8.0), AND 70-100 MM LI2SO4 OR NA2SO4	Resolution 2.70 Å R-free 0.242

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 2VPV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6QLD Structure of inner kinetochore CCAN-Cenp-A complex Deposited 2019-01-31	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 × 20 PDB declaration: 22-meric	Chain C 284–305（22 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.15 Å

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

View Construct and Data Evidence

UniProt name	MIF2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–166； UniProt 365–530 Author chain B； PDBConstruct 1–166； UniProt 365–530

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vpv
Deposition date deposition_date	2008-03-05
Structure title title	Dimerization Domain of Mif2p
Keywords keywords	;NUCLEUS, MITOSIS, CENTROMERE, CELL CYCLE, DNA-BINDING, KINETOCHORE, CELL DIVISION, PHOSPHOPROTEIN, JELLY-ROLL FOLD, DIMERIZATION DOMAIN ;; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.19 Å
Radius of gyration Rg (electron density) rg_electron	16.88 Å
Forward intensity I(0) i0	7526920.00
Molecular weight molecular_weight	21147.0 kDa
Excluded volume excluded_volume	26971 Å³
Envelope volume envelope_volume	31214 Å³
Hydration-shell volume shell_volume	15679 Å³
Envelope diameter envelope_diameter	56.9 Å
Shell Rg shell_rg	22.56 Å
Envelope Rg envelope_rg	17.19 Å
Shape Rg shape_rg	16.82 Å
Total Rg total_rg	18.11 Å
Total atoms total_atoms	1492
Residues n_residues	186
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	57.8 Å
Rg (real space) rg_real	18.12 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	7.5270e+06
I(0) uncertainty (real space) i0_real_error	8.4470e+04
Rg (reciprocal space) rg_reciprocal	18.13 Å
I(0) (reciprocal space) i0_reciprocal	7527000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.196
Kurtosis Kurtosis kurtosis	-0.466
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1296000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.992

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN MIF2
Molecular weight formula_weight	18721.1 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	1519

DPNAKENLIPEDPNEDIIERIESGGIENGEWLKHGILEANVKISDTKEETKDEIIAFAPNLSQTEQVKDTKDENFALEIMFDKHKEYFASGILKLPAISGQKKLSNSFRTYITFHVIQGIVEVTVCKNKFLSVKGSTFQIPAFNEYAIANRGNDEAKMFFVQVTVS

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vpvA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

Domain ID domain_id	2vpvB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

▶

8. Citations (1)

▶

Unit-cell length a length_a	106.020 Å
Unit-cell length b length_b	106.020 Å
Unit-cell length c length_c	106.020 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	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2100
R_work r_work	0.2080
R_free r_free	0.2420

fit	/app/data/saxs_computation/vp/2vpv/2vpv.fit
pddf	/app/data/pr_computation/vp/2vpv/2vpv.pr.out
profile	/app/data/saxs_computation/vp/2vpv/2vpv.dat

Dimerization Domain of Mif2p

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

PROTEIN MIF2

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