1dm3

ACETYLATED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH ACETYL-COA

Method: X-RAY DIFFRACTION Dmax: 121.0 Å Quality: EXCELLENT

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

BIOSYNTHETIC THIOLASE ACETYLATED AT CYS89

Zoogloea ramigera

UniProt P07097

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 5–392 Chain B; UniProt 5–392 Chain C; UniProt 5–392 Chain D; UniProt 5–392 Fragment:ENTIRE THIOLASE, ACETYLATED AT CYS89 Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 ACO ACETYL COENZYME *A × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;0.9 M Ammonium sulfate, 1 M lithium sulfate, 0,1 M sodium acetate, 1 mM DTT, 1mM EDTA, 1mM sodium azide, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.00 Å R-free 0.256

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIL_ZOORA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–389; UniProt 5–392 Author chain B; PDBConstruct 1–389; UniProt 5–392 Author chain C; PDBConstruct 1–389; UniProt 5–392 Author chain D; PDBConstruct 1–389; UniProt 5–392

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1dm3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dm3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dm3
Deposition date deposition_date1999-12-13
Structure title titleACETYLATED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH ACETYL-COA
Keywords keywordsBIOSYNTHETIC THIOLASE, REACTION INTERMEDIATE, ACETYL-COA, BETA-ALPHA FOLD, ACETYL-COA ACETYLTRANSFERASE, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.52
Radius of gyration Rg (electron density) rg_electron37.14
Forward intensity I(0) i0449525000.00
Molecular weight molecular_weight164830.0 kDa
Excluded volume excluded_volume203180 ų
Envelope volume envelope_volume249350 ų
Hydration-shell volume shell_volume54609 ų
Envelope diameter envelope_diameter119.1
Shell Rg shell_rg44.49
Envelope Rg envelope_rg36.65
Shape Rg shape_rg37.15
Total Rg total_rg37.49
Total atoms total_atoms11498
Residues n_residues1552
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax121.0
Rg (real space) rg_real37.45
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real4.4950e+08
I(0) uncertainty (real space) i0_real_error8.2790e+06
Rg (reciprocal space) rg_reciprocal37.50
I(0) (reciprocal space) i0_reciprocal449500000.0000
Solution quality estimate total_estimate0.9015
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.4
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.662
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha151000000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.945

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1dm3a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd1dm3a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd1dm3b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd1dm3b2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd1dm3c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd1dm3c2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd1dm3d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related
Domain ID domain_idd1dm3d2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.1 — Thiolase-related

CATH v4.4 (8 domains)

Domain ID domain_id1dm3A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id1dm3A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id1dm3B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id1dm3B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id1dm3C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id1dm3C02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id1dm3D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id1dm3D02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase

8. Citations (3)

9. Files and Curves (10)