1dlu

UNLIGANDED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA

Method: X-RAY DIFFRACTION Dmax: 117.2 Å Quality: GOOD

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

BIOSYNTHETIC THIOLASE

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 4–391 Chain B; UniProt 4–391 Chain C; UniProt 4–391 Chain D; UniProt 4–391 Not recorded SO4 SULFATE ION × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;AMMONIUM SULPHATE, LITHIUM SULPHATE, SODIUM ACETATE, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.25 Å R-free 0.263

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 4–391 Author chain B; PDBConstruct 1–389; UniProt 4–391 Author chain C; PDBConstruct 1–389; UniProt 4–391 Author chain D; PDBConstruct 1–389; UniProt 4–391

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 1dlu

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1dlu
Deposition date deposition_date1999-12-12
Structure title titleUNLIGANDED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA
Keywords keywordsTHIOLASE FOLD, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.01
Radius of gyration Rg (electron density) rg_electron37.50
Forward intensity I(0) i0421904000.00
Molecular weight molecular_weight161890.0 kDa
Excluded volume excluded_volume200570 ų
Envelope volume envelope_volume249930 ų
Hydration-shell volume shell_volume54373 ų
Envelope diameter envelope_diameter119.8
Shell Rg shell_rg44.72
Envelope Rg envelope_rg36.90
Shape Rg shape_rg37.50
Total Rg total_rg37.89
Total atoms total_atoms11314
Residues n_residues1556
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 dmax117.2
Rg (real space) rg_real37.94
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real4.2190e+08
I(0) uncertainty (real space) i0_real_error6.9020e+06
Rg (reciprocal space) rg_reciprocal37.99
I(0) (reciprocal space) i0_reciprocal421900000.0000
Solution quality estimate total_estimate0.8829
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.3
Skewness Skewness skewness0.199
Kurtosis Kurtosis kurtosis-0.710
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha147600000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.600

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_idd1dlua1
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_idd1dlua2
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_idd1dlub1
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_idd1dlub2
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_idd1dluc1
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_idd1dluc2
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_idd1dlud1
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_idd1dlud2
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_id1dluA01
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_id1dluA02
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_id1dluB01
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_id1dluB02
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_id1dluC01
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_id1dluC02
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_id1dluD01
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_id1dluD02
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 (2)

9. Files and Curves (10)