SAXSdb — 2yyb

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

Hypothetical protein TTHA1606

Thermus thermophilus

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
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SHX4_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 1–242 Author chain B； PDBConstruct 1–242； UniProt 1–242

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	2yyb
Deposition date deposition_date	2007-04-28
Structure title title	Crystal structure of TTHA1606 from Thermus thermophilus HB8
Keywords keywords	;Thermus thermophilus, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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.

2yyb__assembly_1__model_1

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

Download this curve (.dat)

2yyb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yyb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.56 Å
Rg (electron density)	36.47 Å
Total Rg	37.21 Å
Atom count	11418
Residues	1452
Excluded volume	203220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yyb__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yyb__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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2yyba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.0 — automated matches

Domain ID domain_id	d2yybb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2yybA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	2yybA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	2yybB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

Domain ID domain_id	2yybB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1
Homologous superfamily homologous superfamily	30 — NIF3 (NGG1p interacting factor 3)-like

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Unit-cell length a length_a	148.186 Å
Unit-cell length b length_b	148.186 Å
Unit-cell length c length_c	196.395 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	42.780 Å
R factor r_factor	—
R_work r_work	0.2390
R_free r_free	0.2830

Description description	Hypothetical protein TTHA1606
Molecular weight formula_weight	26866.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3826

Crystal structure of TTHA1606 from Thermus thermophilus HB8

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

Hypothetical protein TTHA1606

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

2yyb__assembly_1__model_1

2yyb__assembly_1__model_1 | I(q)

2yyb__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

Crystal structure of TTHA1606 from Thermus thermophilus HB8

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

Hypothetical protein TTHA1606

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

2yyb__assembly_1__model_1

2yyb__assembly_1__model_1 | I(q)

2yyb__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)