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5lvz

Crystal structure of yeast 14-3-3 protein from Lachancea thermotolerans

Method: X-RAY DIFFRACTION Dmax: 68.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

KLTH0G14146p

Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)

UniProt C5DN49

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 1–253 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；13% PEG 3350, 190 mM CaCl2, 3% glycerol Resolution 1.95 Å R-free 0.223

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 5LVZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LX2 Lt 14-3-3 in complex with PI4KIIIB peptide Deposited 2016-09-19 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–253（253 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；MES, PEG 8000, ethylene glycol
Resolution 2.58 Å R-free 0.263

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

View Construct and Data Evidence
UniProt name C5DN49_LACTC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–253； UniProt 1–253

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 5lvz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lvz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5lvz
Deposition date deposition_date2016-09-14
Structure title titleCrystal structure of yeast 14-3-3 protein from Lachancea thermotolerans
Keywords keywords14-3-3, signaling protein; SIGNALING PROTEIN
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_guinier20.25 Å
Radius of gyration Rg (electron density) rg_electron19.28 Å
Forward intensity I(0) i012945600.00
Molecular weight molecular_weight26583.0 kDa
Excluded volume excluded_volume33155 ų
Envelope volume envelope_volume39283 ų
Hydration-shell volume shell_volume17572 ų
Envelope diameter envelope_diameter72.6 Å
Shell Rg shell_rg25.03 Å
Envelope Rg envelope_rg19.64 Å
Shape Rg shape_rg19.26 Å
Total Rg total_rg20.19 Å
Total atoms total_atoms1869
Residues n_residues235
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 dmax68.8 Å
Rg (real space) rg_real20.22 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real1.2950e+07
I(0) uncertainty (real space) i0_real_error1.5940e+05
Rg (reciprocal space) rg_reciprocal20.23 Å
I(0) (reciprocal space) i0_reciprocal12950000.0000
Solution quality estimate total_estimate0.8000
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary26.5 Å
Skewness Skewness skewness0.309
Kurtosis Kurtosis kurtosis-0.184
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2311000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.802; Stabil: 1.000; 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 (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5lvza_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.7 — 14-3-3 protein
Family Family familya.118.7.1 — 14-3-3 protein

CATH v4.4 (1 domains)

Domain ID domain_id5lvzA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain
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8. Citations (1)

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9. Files and Curves (10)