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1ct5

CRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YBL036C-SELENOMET CRYSTAL

Method: X-RAY DIFFRACTION Dmax: 64.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (YEAST HYPOTHETICAL PROTEIN, SELENOMET)

Saccharomyces cerevisiae

UniProt P38197

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–257 Non-standard monomer：Yes (specific site not provided by mmCIF) PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；30% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, 2.9 mg/ml protein in 6.25mM HEPES and 62.5mM NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K Resolution 2.00 Å R-free 0.245

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 1CT5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B54 CRYSTAL STRUCTURE OF A YEAST HYPOTHETICAL PROTEIN-A STRUCTURE FROM BNL'S HUMAN PROTEOME PROJECT Deposited 1999-01-12 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–257（257 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.6
Resolution 2.10 Å R-free 0.303

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name YBD6_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–256； UniProt 2–257

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 1ct5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ct5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ct5
Deposition date deposition_date1999-08-18
Structure title titleCRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YBL036C-SELENOMET CRYSTAL
Keywords keywords;TIM BARREL, YEAST, PYRIDOXAL-5'-PHOSPHATE, SELENOMETHIONINE, MAD, STRUCTURAL GENOMICS, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC ;; STRUCTURAL GENOMICS
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_guinier18.68 Å
Radius of gyration Rg (electron density) rg_electron17.61 Å
Forward intensity I(0) i011916800.00
Molecular weight molecular_weight26126.0 kDa
Excluded volume excluded_volume32818 ų
Envelope volume envelope_volume37705 ų
Hydration-shell volume shell_volume17779 ų
Envelope diameter envelope_diameter61.1 Å
Shell Rg shell_rg23.75 Å
Envelope Rg envelope_rg17.98 Å
Shape Rg shape_rg17.64 Å
Total Rg total_rg18.46 Å
Total atoms total_atoms1827
Residues n_residues225
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 dmax64.9 Å
Rg (real space) rg_real18.59 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real1.1920e+07
I(0) uncertainty (real space) i0_real_error1.5310e+05
Rg (reciprocal space) rg_reciprocal18.61 Å
I(0) (reciprocal space) i0_reciprocal11920000.0000
Solution quality estimate total_estimate0.7864
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.2 Å
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.405
Angular range angular_range— – 0.4250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4160000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.744; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ct5a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.6 — PLP-binding barrel
Family Family familyc.1.6.2 — 'Hypothetical' protein ybl036c

CATH v4.4 (1 domains)

Domain ID domain_id1ct5A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily10 — Alanine racemase
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8. Citations (1)

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9. Files and Curves (10)