1jx7

Crystal structure of ychN protein from E.coli

Method: X-RAY DIFFRACTION

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

HYPOTHETICAL PROTEIN YCHN

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YCHN_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 1–117 Author chain B； PDBConstruct 1–117； UniProt 1–117 Author chain C； PDBConstruct 1–117； UniProt 1–117 Author chain D； PDBConstruct 1–117； UniProt 1–117 Author chain E； PDBConstruct 1–117； UniProt 1–117 Author chain F； PDBConstruct 1–117； UniProt 1–117

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	1jx7
Deposition date deposition_date	2001-09-05
Structure title title	Crystal structure of ychN protein from E.coli
Keywords keywords	;NEW FOLD, HEXAMER, STRUCTURAL GENOMICS, BSGC structure funded by NIH, Protein Structure Initiative, PSI, Berkeley Structural Genomics Center, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1jx7__assembly_1__model_1

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

Download this curve (.dat)

1jx7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jx7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.44 Å
Rg (electron density)	24.13 Å
Total Rg	25.06 Å
Atom count	5334
Residues	684
Excluded volume	96597 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jx7__assembly_1__model_1`	hexameric （6）	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 (2)

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1jx7a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d1jx7a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jx7b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d1jx7b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jx7c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d1jx7c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jx7d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d1jx7d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jx7e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d1jx7e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jx7f1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d1jx7f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	1jx7A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	1jx7B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	1jx7C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	1jx7D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	1jx7E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	1jx7F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

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Unit-cell length a length_a	66.210 Å
Unit-cell length b length_b	80.460 Å
Unit-cell length c length_c	140.150 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 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.980 Å
R factor r_factor	0.2290
R_work r_work	0.2290
R_free r_free	0.2650

Description description	HYPOTHETICAL PROTEIN YCHN
Molecular weight formula_weight	12843.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5420

Crystal structure of ychN protein from E.coli

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

HYPOTHETICAL PROTEIN YCHN

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

1jx7__assembly_1__model_1

1jx7__assembly_1__model_1 | I(q)

1jx7__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

Crystal structure of ychN protein from E.coli

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

HYPOTHETICAL PROTEIN YCHN

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

1jx7__assembly_1__model_1

1jx7__assembly_1__model_1 | I(q)

1jx7__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)