SAXSdb — 1jop

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

Yhch protein

Haemophilus influenzae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MERCURY (II) ION × 6 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	MERCURY (II) ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y227_HAEIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–155； UniProt 1–155 Author chain B； PDBConstruct 1–155； UniProt 1–155 Author chain C； PDBConstruct 1–155； UniProt 1–155 Author chain D； PDBConstruct 1–155； UniProt 1–155

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	1jop
Deposition date deposition_date	2001-07-30
Structure title title	YHCH protein (HI0227)
Keywords keywords	structural genomics, beta-sandwich, Structure 2 Function Project, S2F, 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.

1jop__assembly_1__model_1

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

Download this curve (.dat)

1jop__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jop__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.02 Å
Rg (electron density)	18.78 Å
Total Rg	19.49 Å
Atom count	2260
Residues	280
Excluded volume	40928 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jop__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jop__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 (3)

Entity 1 Entity 1 polymer

Description description	Yhch protein
Molecular weight formula_weight	17691.3 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	4598

MIISSLTNPNFKVGLPKVIAEVCDYLNTLDLNALENGRHDINDQIYMNVMEPETAEPSSKKAELHHEYLDVQVLIRGTENIEVGATYPNLSKYEDYNEADDYQLCADIDDKFTVTMKPKMFAVFYPYEPHKPCCVVNGKTEKIKKLVVKVPVKLI

Source Source

Source organism organism	Haemophilus influenzae
NCBI taxonomy ID ncbi_taxonomy_id	727
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1jopa_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.7 — YhcH-like

Domain ID domain_id	d1jopb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.7 — YhcH-like

Domain ID domain_id	d1jopc_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.7 — YhcH-like

Domain ID domain_id	d1jopd_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.7 — YhcH-like

CATH v4.4 (4 domains)

Domain ID domain_id	1jopA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	370 — YhcH/YjgK/YiaL

Domain ID domain_id	1jopB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	370 — YhcH/YjgK/YiaL

Domain ID domain_id	1jopC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	370 — YhcH/YjgK/YiaL

Domain ID domain_id	1jopD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	370 — YhcH/YjgK/YiaL

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Unit-cell length a length_a	43.100 Å
Unit-cell length b length_b	152.300 Å
Unit-cell length c length_c	53.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.60 °
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	2.600 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	—

YHCH protein (HI0227)

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

Yhch protein

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

1jop__assembly_1__model_1

1jop__assembly_1__model_1 | I(q)

1jop__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

YHCH protein (HI0227)

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

Yhch protein

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

1jop__assembly_1__model_1

1jop__assembly_1__model_1 | I(q)

1jop__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)