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4gp9

Crystal Structure of Benzoylformate Decarboxylase Mutant L403F

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

Benzoylformate decarboxylase

Pseudomonas putida

UniProt P20906

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 CALCIUM ION × 8 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE × 4 GLYCEROL × 8 SODIUM ION × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
8xbo 8xbq 8xbr

3 assemblies

Homodimer

None

Homotetramer
1bfd 1mcz 1mcz 1mcz 1mcz 1pi3 1po7 1q6z 1yno 2fn3 2fwn 2v3w

49 assemblies; showing the first 12

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name MDLC_PSEPU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–528； UniProt 1–528

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_id4gp9
Deposition date deposition_date2012-08-20
Structure title titleCrystal Structure of Benzoylformate Decarboxylase Mutant L403F
Keywords keywordsDECARBOXYLASE, THIAMIN THIAZOLONE DIPHOSPHATE COFACTOR, LYASE; LYASE
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.

4gp9__assembly_1__model_1

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

Download this curve (.dat)

4gp9__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.

4gp9__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）36.92 Å
Rg (electron density)35.92 Å
Total Rg36.55 Å
Atom count15942
Residues2100
Excluded volume282730 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4gp9__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 (6)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4gp9a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches
Domain ID domain_idd4gp9a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd4gp9a3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id4gp9A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id4gp9A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4gp9A03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
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7. Citations (1)