SAXSdb — 1v8f

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

Pantoate-beta-alanine ligase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 5 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 1 HEXAETHYLENE GLYCOL × 1 GLYCEROL × 8 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CHLORIDE ION × 10 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 2 HEXAETHYLENE GLYCOL × 2 GLYCEROL × 16 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P83701_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 1–276 Author chain B； PDBConstruct 1–276； UniProt 1–276

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	1v8f
Deposition date deposition_date	2004-01-08
Structure title title	Crystal Structure of Pantoate-beta-Alanine (Pantothenate Synthetase) from Thermus Thermophilus HB8
Keywords keywords	Ligase, Rossmann Fold, Dimer, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI; LIGASE
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.

1v8f__assembly_1__model_1

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

Download this curve (.dat)

1v8f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v8f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.14 Å
Rg (electron density)	27.30 Å
Total Rg	27.96 Å
Atom count	4420
Residues	552
Excluded volume	79031 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v8f__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1v8f__assembly_2__model_1`	tetrameric （4）	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	Pantoate-beta-alanine ligase
Molecular weight formula_weight	30733.3 kDa
EC 编号 ec_number	6.3.2.1
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	5144

MRTVSTVAELRAALPREGVGFVPTMGYLHRGHLALVERARRENPFVVVSVFVNPLQFGPGEDYHRYPRDLERDRALLQEAGVDLLFAPGVEEMYPEGFATRVQVEGPLTALWEGAVRPGHFQGVATVVARLFLLVQPQRAYFGEKDYQQLLVVRRMVRDLGFPVEVVGVPTVREEDGLALSSRNVYLSPETRKKAPVLYRALLAMREVAGQGGSVAEALRAGEEALRAVPEFRKDYLAIVHPETLLPLSDWVAGARGIVAGRFPEARLIDNLEVYP

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	724

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1v8fa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.4 — Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)

Domain ID domain_id	d1v8fb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.4 — Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)

CATH v4.4 (4 domains)

Domain ID domain_id	1v8fA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1v8fA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
Homologous superfamily homologous superfamily	10 — Pantoate-beta-alanine ligase, C-terminal domain

Domain ID domain_id	1v8fB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1v8fB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
Homologous superfamily homologous superfamily	10 — Pantoate-beta-alanine ligase, C-terminal domain

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Unit-cell length a length_a	88.514 Å
Unit-cell length b length_b	88.514 Å
Unit-cell length c length_c	266.720 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	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2050
R_free r_free	0.2570

Crystal Structure of Pantoate-beta-Alanine (Pantothenate Synthetase) from Thermus Thermophilus HB8

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

Pantoate-beta-alanine ligase

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

1v8f__assembly_1__model_1

1v8f__assembly_1__model_1 | I(q)

1v8f__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Pantoate-beta-Alanine (Pantothenate Synthetase) from Thermus Thermophilus HB8

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

Pantoate-beta-alanine ligase

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

1v8f__assembly_1__model_1

1v8f__assembly_1__model_1 | I(q)

1v8f__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)