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4m6v

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

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PYRUVATE CARBOXYLASE

Rhizobium etli

UniProt Q2K340

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 MAGNESIUM ION × 4 CHLORIDE ION × 4 PYRUVIC ACID × 4 Biocytin × 8 GLYCEROL × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
4jx4 4jx4 4jx5 4jx5 4jx6 4jx6

6 assemblies

Homotetramer
2qf7 3tw6 3tw6 3tw7 4jx4 4jx5 4jx6 4loc 4m6v 4mfd 4mfe 4mim

12 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

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_id4m6v
Deposition date deposition_date2013-08-11
Structure title titleStructure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin
Keywords keywordsTIM Barrel, Ligase; LIGASE
Experimental Method methodX-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.

4m6v__assembly_1__model_1

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

Download this curve (.dat)

4m6v__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4m6v__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）50.08 Å
Rg (electron density)49.96 Å
Total Rg50.17 Å
Atom count18044
Residues2375
Excluded volume320800 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4m6v__assembly_1__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 (8)

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id4m6vA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily10 — pyruvate carboxylase f1077a mutant domain
Domain ID domain_id4m6vA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id4m6vA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily90 — Conserved carboxylase domain
Domain ID domain_id4m6vA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4m6vB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily10 — pyruvate carboxylase f1077a mutant domain
Domain ID domain_id4m6vB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id4m6vB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily90 — Conserved carboxylase domain
Domain ID domain_id4m6vB04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4m6vC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily10 — pyruvate carboxylase f1077a mutant domain
Domain ID domain_id4m6vC02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id4m6vC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily90 — Conserved carboxylase domain
Domain ID domain_id4m6vC04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id4m6vD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology600 — pyruvate carboxylase f1077a mutant fold
Homologous superfamily homologous superfamily10 — pyruvate carboxylase f1077a mutant domain
Domain ID domain_id4m6vD02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id4m6vD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily90 — Conserved carboxylase domain
Domain ID domain_id4m6vD04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
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7. Citations (1)