SAXSdb — 4ixn

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

Uncharacterized GTP-binding protein YjiA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 SULFATE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 3 SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YJIA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–318； UniProt 1–318 Author chain B； PDBConstruct 1–318； UniProt 1–318

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	4ixn
Deposition date deposition_date	2013-01-26
Structure title title	Crystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant YjiA GTPase
Keywords keywords	P-loop GTPase, G-protein, metal homeostasis, HYDROLASE; HYDROLASE
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.

4ixn__assembly_1__model_1

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

Download this curve (.dat)

4ixn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ixn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.51 Å
Rg (electron density)	25.23 Å
Total Rg	25.97 Å
Atom count	4824
Residues	636
Excluded volume	85902 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ixn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ixn__assembly_2__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Uncharacterized GTP-binding protein YjiA
Molecular weight formula_weight	35574.4 kDa
Mutation mutation	E37A, C66A, C67A
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	5158

MNPIAVTLLTGFLGAGKTTLLRHILNEQHGYKIAVIANEFGEVSVDDQLIGDRATQIKTLTNGCIAASRSNELEDALLDLLDNLDKGNIQFDRLVIECTGMADPGPIIQTFFSHEVLCQRYLLDGVIALVDAVHADEQMNQFTIAQSQVGYADRILLTKTDVAGEAEKLHERLARINARAPVYTVTHGDIDLGLLFNTNGFMLEENVVSTKPRFHFIADKQNDISSIVVELDYPVDISEVSRVMENLLLESADKLLRYKGMLWIDGEPNRLLFQGVQRLYSADWDRPWGDEKPHSTMVFIGIQLPEEEIRAAFAGLRK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	256

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ixna1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

Domain ID domain_id	d4ixna2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.237 — Hypothetical protein YjiA, C-terminal domain
Superfamily Superfamily superfamily	d.237.1 — Hypothetical protein YjiA, C-terminal domain
Family Family family	d.237.1.1 — Hypothetical protein YjiA, C-terminal domain

Domain ID domain_id	d4ixnb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.10 — Nitrogenase iron protein-like

Domain ID domain_id	d4ixnb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.237 — Hypothetical protein YjiA, C-terminal domain
Superfamily Superfamily superfamily	d.237.1 — Hypothetical protein YjiA, C-terminal domain
Family Family family	d.237.1.1 — Hypothetical protein YjiA, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	4ixnA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4ixnA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1220 — Hypothetical Protein Yjia; Chain: A;domain 2
Homologous superfamily homologous superfamily	10 — CobW-like, C-terminal domain

Domain ID domain_id	4ixnB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4ixnB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1220 — Hypothetical Protein Yjia; Chain: A;domain 2
Homologous superfamily homologous superfamily	10 — CobW-like, C-terminal domain

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Unit-cell length a length_a	56.071 Å
Unit-cell length b length_b	68.436 Å
Unit-cell length c length_c	77.699 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	75.300 Å
R factor r_factor	0.2044
R_work r_work	0.2027
R_free r_free	0.2381

Crystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant YjiA GTPase

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

Uncharacterized GTP-binding protein YjiA

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

4ixn__assembly_1__model_1

4ixn__assembly_1__model_1 | I(q)

4ixn__assembly_1__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant YjiA GTPase

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

Uncharacterized GTP-binding protein YjiA

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

4ixn__assembly_1__model_1

4ixn__assembly_1__model_1 | I(q)

4ixn__assembly_1__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)