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5xw5

Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide

Method: X-RAY DIFFRACTION Dmax: 98.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tyrosine-protein phosphatase CDC14

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q00684

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–374 Fragment：UNP residues 1-374 Mutation：C283S Regulatory protein SWI6 × 1 （P09959） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Bis-Tris, ammonium sulfate, PEG 4000 Resolution 1.85 Å R-free 0.217
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–374 Fragment：UNP residues 1-374 Mutation：C283S SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Bis-Tris, ammonium sulfate, PEG 4000 Resolution 1.85 Å R-free 0.217

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 5XW5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4ZJ7 Crystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p Deposited 2015-04-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 517–551（35 aa） Fragment：UNP residues 517-551
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 20000, 2-propanol
Resolution 2.40 Å R-free 0.252
5XW4 Crystal structure of budding yeast Cdc14p (wild type) in the apo state Deposited 2017-06-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa） Fragment：UNP residues 1-374
Chain B 1–374（374 aa） Fragment：UNP residues 1-374
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Bis-Tris, ammonium sulfate, PEG4000
Resolution 1.85 Å R-free 0.203
6G84 Structure of Cdc14 bound to CBK1 PxL motif Deposited 2018-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded CA CALCIUM ION × 4 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；11% PEG3350, 0.2M Calcium Acetate
Resolution 2.47 Å R-free 0.270
6G85 Structure of Cdc14 bound to CBK1 PxL motif Deposited 2018-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；1.5% PEG 6000 and 0.1 M MES pH 6.0
Resolution 1.53 Å R-free 0.209
6G86 Structure of Cdc14 bound to SIC1 PxL motif Deposited 2018-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 P6G HEXAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 5 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH6, 18% PEG200, 5% PEG 3000
Resolution 1.74 Å R-free 0.199

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDC14_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 42–415； UniProt 1–374 Author chain B； PDBConstruct 42–415； UniProt 1–374

Regulatory protein SWI6

OrganismNot specified

UniProt P09959

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 155–164 Fragment：UNP residues 155-164 Non-standard monomer：Yes (specific site not provided by mmCIF) Tyrosine-protein phosphatase CDC14 × 1 （Q00684） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Bis-Tris, ammonium sulfate, PEG 4000 Resolution 1.85 Å R-free 0.217

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 5XW5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1SW6 S. CEREVISIAE SWI6 ANKYRIN-REPEAT FRAGMENT Deposited 1998-09-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 188–512（325 aa） Fragment：ANKYRIN-REPEAT DOMAIN
Chain B 188–512（325 aa） Fragment：ANKYRIN-REPEAT DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.50
Resolution 2.10 Å R-free 0.251
2XFV Structure of the amino-terminal domain from the cell-cycle regulator Swi6 Deposited 2010-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–126（125 aa） Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 2-126
Chain B 2–126（125 aa） Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 2-126
Not recorded CA CALCIUM ION × 3 GOL GLYCEROL × 3 ACT ACETATE ION × 1 CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；5-15MG/ML PROTEIN, 10% PEG4000, 0.1M NA-CACODYLATE, 20MM CA-ACETATE, 0.2M NH4CL, PH 6.5
Resolution 1.90 Å R-free 0.196

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

View Construct and Data Evidence
UniProt name SWI6_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–10； UniProt 155–164

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 5xw5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xw5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xw5
Deposition date deposition_date2017-06-29
Structure title titleCrystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide
Keywords keywordsphosphatase, CELL CYCLE; CELL CYCLE
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_guinier29.08 Å
Radius of gyration Rg (electron density) rg_electron28.09 Å
Forward intensity I(0) i0106440000.00
Molecular weight molecular_weight83675.0 kDa
Excluded volume excluded_volume105380 ų
Envelope volume envelope_volume125190 ų
Hydration-shell volume shell_volume36757 ų
Envelope diameter envelope_diameter107.4 Å
Shell Rg shell_rg35.90 Å
Envelope Rg envelope_rg28.59 Å
Shape Rg shape_rg28.10 Å
Total Rg total_rg28.80 Å
Total atoms total_atoms5922
Residues n_residues733
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 dmax98.8 Å
Rg (real space) rg_real29.01 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real1.0640e+08
I(0) uncertainty (real space) i0_real_error1.6510e+06
Rg (reciprocal space) rg_reciprocal29.04 Å
I(0) (reciprocal space) i0_reciprocal106400000.0000
Solution quality estimate total_estimate0.6631
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.1 Å
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.425
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33260000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.977; Smooth: 0.952
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)