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1afw

THE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE

Method: X-RAY DIFFRACTION Dmax: 84.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

3-KETOACETYL-COA THIOLASE

OrganismNot specified

UniProt P27796

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 25–417 Chain B； UniProt 25–417 Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：microdiaylsis；pH 6.5；293 K；MICRODIALYSIS AGAINST 25MM MOPS PH6.5, 200MM DTT, 1MM EDTA, 1MM SODIUM AZIDE, AT 20 DEGREES CELSIUS, microdiaylsis, temperature 293K Resolution 1.80 Å R-free 0.240

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.

Other PDB Difference from Current Entry 1AFW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1PXT THE 2.8 ANGSTROMS STRUCTURE OF PEROXISOMAL 3-KETOACYL-COA THIOLASE OF SACCHAROMYCES CEREVISIAE: A FIVE LAYERED A-B-A-B-A STRUCTURE, CONSTRUCTED FROM TWO CORE DOMAINS OF IDENTICAL TOPOLOGY Deposited 1994-07-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–417（390 aa）
Chain B 28–417（390 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions THE PROTEIN HAS BEEN CRYSTALLIZED IN THE ABSENCE OF AN ACTIVE SITE LIGAND.
Resolution 2.80 Å R-free 0.334
3W15 Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with Pex7p and Pex21p Deposited 2012-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–15（15 aa） Fragment：UNP residue 1-15, UNP residues 27-396
Not recorded NO3 NITRATE ION × 9 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；293 K；25% PEG2000, 0.3M Magnesium nitrate, 0.1M Tris-HCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.224

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIK_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–393； UniProt 25–417 Author chain B； PDBConstruct 1–393； UniProt 25–417

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 1afw

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1afw
Deposition date deposition_date1997-03-15
Structure title titleTHE 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE DIMERIC PEROXISOMAL THIOLASE OF SACCHAROMYCES CEREVISIAE
Keywords keywordsTHIOLASE, FATTY ACID METABOLISM; THIOLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.58 Å
Radius of gyration Rg (electron density) rg_electron25.55 Å
Forward intensity I(0) i0111749000.00
Molecular weight molecular_weight83899.0 kDa
Excluded volume excluded_volume105390 ų
Envelope volume envelope_volume119180 ų
Hydration-shell volume shell_volume37198 ų
Envelope diameter envelope_diameter90.5 Å
Shell Rg shell_rg34.33 Å
Envelope Rg envelope_rg25.87 Å
Shape Rg shape_rg25.57 Å
Total Rg total_rg26.33 Å
Total atoms total_atoms5890
Residues n_residues783
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax84.5 Å
Rg (real space) rg_real26.48 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real1.1170e+08
I(0) uncertainty (real space) i0_real_error1.6730e+06
Rg (reciprocal space) rg_reciprocal26.51 Å
I(0) (reciprocal space) i0_reciprocal111800000.0000
Solution quality estimate total_estimate0.8933
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.4 Å
Skewness Skewness skewness0.279
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33210000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.972
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1afwa1
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_idd1afwa2
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_idd1afwb1
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_idd1afwb2
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 (4 domains)

Domain ID domain_id1afwA01
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_id1afwA02
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_id1afwB01
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_id1afwB02
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
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8. Citations (1)

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9. Files and Curves (10)