1vrq

Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid

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

Sarcosine oxidase alpha subunit

Corynebacterium sp.

UniProt Q50LF0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Sarcosine oxidase beta subunit × 1 (Q50LF2) Sarcosine oxidase gamma subunit × 1 (Q50LE9) Sarcosine oxidase delta subunit × 1 (Q50LF1) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q50LF0_9CORY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–964; UniProt 2–965

Sarcosine oxidase beta subunit

Corynebacterium sp.

UniProt Q50LF2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Sarcosine oxidase alpha subunit × 1 (Q50LF0) Sarcosine oxidase gamma subunit × 1 (Q50LE9) Sarcosine oxidase delta subunit × 1 (Q50LF1) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase gamma subunit × 2 (Q50LE9) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q50LF2_9CORY
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–404; UniProt 2–405

Sarcosine oxidase gamma subunit

Corynebacterium sp.

UniProt Q50LE9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Sarcosine oxidase alpha subunit × 1 (Q50LF0) Sarcosine oxidase beta subunit × 1 (Q50LF2) Sarcosine oxidase delta subunit × 1 (Q50LF1) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase delta subunit × 2 (Q50LF1) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q50LE9_9CORY
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–200; UniProt 6–205

Sarcosine oxidase delta subunit

Corynebacterium sp.

UniProt Q50LF1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Sarcosine oxidase alpha subunit × 1 (Q50LF0) Sarcosine oxidase beta subunit × 1 (Q50LF2) Sarcosine oxidase gamma subunit × 1 (Q50LE9) SULFATE ION × 13 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 FLAVIN MONONUCLEOTIDE × 1 N,N-DIMETHYLGLYCINE × 1 ZINC ION × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 8 Sarcosine oxidase alpha subunit × 2 (Q50LF0) Sarcosine oxidase beta subunit × 2 (Q50LF2) Sarcosine oxidase gamma subunit × 2 (Q50LE9) SULFATE ION × 26 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid × 2 FLAVIN-ADENINE DINUCLEOTIDE × 2 FLAVIN MONONUCLEOTIDE × 2 N,N-DIMETHYLGLYCINE × 2 ZINC ION × 2 water × 8 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name Q50LF1_9CORY
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–99; UniProt 1–99

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_id1vrq
Deposition date deposition_date2005-04-27
Structure title titleCrystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid
Keywords keywordsHeterotetrameric sarcosine oxidase, flavoenzyme, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

1vrq__assembly_3__model_1

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

Download this curve (.dat)

1vrq__assembly_3__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1vrq__assembly_3__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)52.27 Å
Rg (electron density)52.57 Å
Total Rg52.62 Å
Atom count25478
Residues3302
Excluded volume448160 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1vrq__assembly_1__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1vrq__assembly_2__model_1 octameric (8) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1vrq__assembly_3__model_1 octameric (8) 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 (12)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id1vrqA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily120 — Probable tRNA modification gtpase trme; domain 1
Domain ID domain_id1vrqB01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1vrqB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — D-Amino Acid Oxidase, subunit A, domain 2
Domain ID domain_id1vrqC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily120 — Probable tRNA modification gtpase trme; domain 1
Domain ID domain_id1vrqC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1520 — Heterotetrameric sarcosine oxidase
Domain ID domain_id1vrqD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2270 — Folate-binding fold
Homologous superfamily homologous superfamily10 — Folate-binding superfamily
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7. Citations (1)