4ybo

Structure of Citrate Synthase from the Thermoacidophilic Euryarchaeon Thermolasma acidophilum

Method: X-RAY DIFFRACTION

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

Citrate synthase

Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CISY_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–384； UniProt 2–385 Author chain B； PDBConstruct 1–384； UniProt 2–385 Author chain C； PDBConstruct 1–384； UniProt 2–385 Author chain D； PDBConstruct 1–384； UniProt 2–385

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	4ybo
Deposition date deposition_date	2015-02-19
Structure title title	Structure of Citrate Synthase from the Thermoacidophilic Euryarchaeon Thermolasma acidophilum
Keywords keywords	Tricarboxylic acid cycle, Transferase, Carbohydrate metabolism; TRANSFERASE
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.

4ybo__assembly_1__model_1

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

Download this curve (.dat)

4ybo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ybo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.01 Å
Rg (electron density)	28.21 Å
Total Rg	28.90 Å
Atom count	6126
Residues	776
Excluded volume	109510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ybo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ybo__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	Citrate synthase
Molecular weight formula_weight	44737.0 kDa
EC 编号 ec_number	2.3.3.16
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	13127

PETEEISKGLEDVNIKWTRLTTIDGNKGILRYGGYSVEDIIASGAQDEEIQYLFLYGNLPTEQELRKYKETVQKGYKIPDFVINAIRQLPRESDAVAMQMAAVAAMAASETKFKWNKDTDRDVAAEMIGRMSAITVNVYRHIMNMPAELPKPSDSYAESFLNAAFGRKATKEEIDAMNTALILYTDHEVPASTTAGLVAVSTLSDMYSGITAALAALKGPLHGGAAEAAIAQFDEIKDPAMVEKWFNDNIINGKKRLMGFGHRVYKTYDPRAKIFKGIAEKLSSKKPEVHKVYEIATKLEDFGIKAFGSKGIYPNTDYFSGIVYMSIGFPLRNNIYTALFALSRVTGWQAHFIEYVEEQQRLIRPRAVYVGPAERKYVPIAERKVDKLAAALEHHHHHH

Source Source

Source organism organism	Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
NCBI taxonomy ID ncbi_taxonomy_id	273075
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	BICARBONATE ION
Molecular weight formula_weight	61.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	868

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4yboa1
Class class	a — All alpha proteins
Fold Fold fold	a.103 — Citrate synthase
Superfamily Superfamily superfamily	a.103.1 — Citrate synthase
Family Family family	a.103.1.1 — Citrate synthase

Domain ID domain_id	d4yboa2
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	d4ybob_
Class class	a — All alpha proteins
Fold Fold fold	a.103 — Citrate synthase
Superfamily Superfamily superfamily	a.103.1 — Citrate synthase
Family Family family	a.103.1.1 — Citrate synthase

Domain ID domain_id	d4yboc_
Class class	a — All alpha proteins
Fold Fold fold	a.103 — Citrate synthase
Superfamily Superfamily superfamily	a.103.1 — Citrate synthase
Family Family family	a.103.1.1 — Citrate synthase

Domain ID domain_id	d4ybod1
Class class	a — All alpha proteins
Fold Fold fold	a.103 — Citrate synthase
Superfamily Superfamily superfamily	a.103.1 — Citrate synthase
Family Family family	a.103.1.1 — Citrate synthase

Domain ID domain_id	d4ybod2
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 (8 domains)

Domain ID domain_id	4yboA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Citrate Synthase, domain 1

Domain ID domain_id	4yboA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome P450-Terp, domain 2

Domain ID domain_id	4yboB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Citrate Synthase, domain 1

Domain ID domain_id	4yboB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome P450-Terp, domain 2

Domain ID domain_id	4yboC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Citrate Synthase, domain 1

Domain ID domain_id	4yboC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome P450-Terp, domain 2

Domain ID domain_id	4yboD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Citrate Synthase, domain 1

Domain ID domain_id	4yboD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome P450-Terp, domain 2

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Unit-cell length a length_a	56.505 Å
Unit-cell length b length_b	113.406 Å
Unit-cell length c length_c	120.066 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.08 °
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	2.179 Å
Low-resolution limit resolution_low	29.148 Å
R factor r_factor	0.1655
R_work r_work	0.1642
R_free r_free	0.2118

Structure of Citrate Synthase from the Thermoacidophilic Euryarchaeon Thermolasma acidophilum

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

Citrate synthase

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

4ybo__assembly_1__model_1

4ybo__assembly_1__model_1 | I(q)

4ybo__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) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of Citrate Synthase from the Thermoacidophilic Euryarchaeon Thermolasma acidophilum

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

Citrate synthase

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

4ybo__assembly_1__model_1

4ybo__assembly_1__model_1 | I(q)

4ybo__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) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)