SAXSdb — 5iit

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

Vacuolar transporter chaperone 4,Core histone macro-H2A.1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 2 MAGNESIUM ION × 1 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2AY_HUMAN
Isoform	O75367-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 182–367； UniProt 181–366 Author chain B； PDBConstruct 182–367； UniProt 181–366 Author chain C； PDBConstruct 182–367； UniProt 181–366 Author chain D； PDBConstruct 182–367； UniProt 181–366

Vacuolar transporter chaperone 4,Core histone macro-H2A.1

Homo sapiens

UniProt P47075

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 1,2-ETHANEDIOL × 2 MAGNESIUM ION × 1 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VTC4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–178； UniProt 1–178 Author chain B； PDBConstruct 1–178； UniProt 1–178 Author chain C； PDBConstruct 1–178； UniProt 1–178 Author chain D； PDBConstruct 1–178； UniProt 1–178

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	5iit
Deposition date deposition_date	2016-03-01
Structure title title	Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1
Keywords keywords	helical bundle, alpha-helical hairpin, inositol phosphate binding protein, protein-protein interaction, chaperone; inositol phosphate binding protein
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5iit__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5iit__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5iit__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.26 Å
Rg (electron density)	32.16 Å
Total Rg	32.46 Å
Atom count	2827
Residues	355
Excluded volume	50645 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5iit__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5iit__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5iit__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5iit__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Vacuolar transporter chaperone 4,Core histone macro-H2A.1
Molecular weight formula_weight	42234.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11622

MKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELDKVYTFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKFSRLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGAGSDGFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGNTLEKKGGKEFVEAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVWGADKCEELLEKTVKNCLALADDKKLKSIAFPSIGSGRNGFPKQTAAQLILKAISSYFVSTMSSSIKTVYFVLFDSESIGIYVQEMAKLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	184

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5iitA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	5iitB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	5iitC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

Domain ID domain_id	5iitD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

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Unit-cell length a length_a	105.640 Å
Unit-cell length b length_b	67.922 Å
Unit-cell length c length_c	129.677 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.134 Å
Low-resolution limit resolution_low	46.859 Å
R factor r_factor	0.2128
R_work r_work	0.2109
R_free r_free	0.2471

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

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

Vacuolar transporter chaperone 4,Core histone macro-H2A.1

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar transporter chaperone 4,Core histone macro-H2A.1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5iit__assembly_4__model_1

5iit__assembly_4__model_1 | I(q)

5iit__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

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

Vacuolar transporter chaperone 4,Core histone macro-H2A.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar transporter chaperone 4,Core histone macro-H2A.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5iit__assembly_4__model_1

5iit__assembly_4__model_1 | I(q)

5iit__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)