4jx5

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate

Method: X-RAY DIFFRACTION

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

Pyruvate carboxylase

Rhizobium etli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 4 CHLORIDE ION × 4 MAGNESIUM ION × 4 PYRUVIC ACID × 4 GLYCEROL × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CHLORIDE ION × 2 MAGNESIUM ION × 2 PYRUVIC ACID × 2 GLYCEROL × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CHLORIDE ION × 2 MAGNESIUM ION × 2 PYRUVIC ACID × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2K340_RHIEC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 30–632； UniProt 465–1067 Author chain B； PDBConstruct 30–632； UniProt 465–1067 Author chain C； PDBConstruct 30–632； UniProt 465–1067 Author chain D； PDBConstruct 30–632； UniProt 465–1067

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	4jx5
Deposition date deposition_date	2013-03-27
Structure title title	Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate
Keywords keywords	TIM Barrel, Ligase, transferase; Ligase,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.

4jx5__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4jx5__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jx5__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	32.47 Å
Rg (electron density)	31.60 Å
Total Rg	32.15 Å
Atom count	8809
Residues	1184
Excluded volume	155850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jx5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4jx5__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4jx5__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Description description	Pyruvate carboxylase
Molecular weight formula_weight	69963.4 kDa
EC 编号 ec_number	6.4.1.1
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	17941

MGSSHHHHHHHHDYDIPTSENLYFQGLLHQQVKRQDRATKLLTYLADVTVNGHPEAKDRPKPLENAARPVVPYANGNGVKDGTKQLLDTLGPKKFGEWMRNEKRVLLTDTTMRDGHQSLLATRMRTYDIARIAGTYSHALPNLLSLECWGGATFDVSMRFLTEDPWERLALIREGAPNLLLQMLLRGANGVGYTNYPDNVVKYFVRQAAKGGIDLFRVFDCLNWVENMRVSMDAIAEENKLCEAAICYTGDILNSARPKYDLKYYTNLAVELEKAGAHIIAVKDMAGLLKPAAAKVLFKALREATGLPIHFHTHDTSGIAAATVLAAVEAGVDAVDAAMDALSGNTSQPCLGSIVEALSGSERDPGLDPAWIRRISFYWEAVRNQYAAFESDLKGPASEVYLHEMPGGQFTNLKEQARSLGLETRWHQVAQAYADANQMFGDIVKVTPSSKVVGDMALMMVSQDLTVADVVSPDREVSFPESVVSMLKGDLGQPPSGWPEALQKKALKGEKPYTVRPGSLLKEADLDAERKVIEKKLEREVSDFEFASYLMYPKVFTDFALASDTYGPVSVLPTPAYFYGLADGEELFADIEKGKTLVIVNQAVSATDSQGMVTVFFELNGQPRRIKVPDRA

Source Source

Source organism organism	Rhizobium etli
NCBI taxonomy ID ncbi_taxonomy_id	347834
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	PYRUVIC ACID
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	207

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	4jx5A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily	10 — pyruvate carboxylase f1077a mutant domain

Domain ID domain_id	4jx5A02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4jx5A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	90 — Conserved carboxylase domain

Domain ID domain_id	4jx5A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	4jx5B01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily	10 — pyruvate carboxylase f1077a mutant domain

Domain ID domain_id	4jx5B02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4jx5B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	90 — Conserved carboxylase domain

Domain ID domain_id	4jx5B04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	4jx5C01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily	10 — pyruvate carboxylase f1077a mutant domain

Domain ID domain_id	4jx5C02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4jx5C03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	90 — Conserved carboxylase domain

Domain ID domain_id	4jx5C04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	4jx5D01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily	10 — pyruvate carboxylase f1077a mutant domain

Domain ID domain_id	4jx5D02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	4jx5D03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	90 — Conserved carboxylase domain

Domain ID domain_id	4jx5D04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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Unit-cell length a length_a	85.130 Å
Unit-cell length b length_b	157.253 Å
Unit-cell length c length_c	245.320 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	46.880 Å
R factor r_factor	0.1889
R_work r_work	0.1866
R_free r_free	0.2321

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate

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

Pyruvate carboxylase

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

4jx5__assembly_3__model_1

4jx5__assembly_3__model_1 | I(q)

4jx5__assembly_3__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate

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

Pyruvate carboxylase

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

4jx5__assembly_3__model_1

4jx5__assembly_3__model_1 | I(q)

4jx5__assembly_3__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)