SAXSdb — 5xw4

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

Tyrosine-protein phosphatase CDC14

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1–374 Chain B； UniProt 1–374	Fragment：UNP residues 1-374	No other associated polymer	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

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 5XW4	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 oligomeric state 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
5XW5 Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide Deposited 2017-06-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–374（374 aa） Fragment：UNP residues 1-374	Mutation：C283S	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, PEG 4000	Resolution 1.85 Å R-free 0.217
5XW5 Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide Deposited 2017-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–374（374 aa） 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
6G84 Structure of Cdc14 bound to CBK1 PxL motif Deposited 2018-04-07	Different construct 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 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 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 6 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5xw4
Deposition date deposition_date	2017-06-29
Structure title title	Crystal structure of budding yeast Cdc14p (wild type) in the apo state
Keywords keywords	phosphatase, CELL CYCLE; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.24 Å
Radius of gyration Rg (electron density) rg_electron	28.20 Å
Forward intensity I(0) i0	107334000.00
Molecular weight molecular_weight	84114.0 kDa
Excluded volume excluded_volume	106010 Å³
Envelope volume envelope_volume	126820 Å³
Hydration-shell volume shell_volume	37051 Å³
Envelope diameter envelope_diameter	108.3 Å
Shell Rg shell_rg	35.96 Å
Envelope Rg envelope_rg	28.68 Å
Shape Rg shape_rg	28.21 Å
Total Rg total_rg	28.93 Å
Total atoms total_atoms	5955
Residues n_residues	737
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	99.4 Å
Rg (real space) rg_real	29.15 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	1.0730e+08
I(0) uncertainty (real space) i0_real_error	1.7980e+06
Rg (reciprocal space) rg_reciprocal	29.19 Å
I(0) (reciprocal space) i0_reciprocal	107300000.0000
Solution quality estimate total_estimate	0.8804
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.450
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	36090000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein phosphatase CDC14
Molecular weight formula_weight	47640.8 kDa
EC 编号 ec_number	3.1.3.48
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6526

MGSSHHHHHHSQDPNSSSARLQVDKLDYDIPTTENLYFQGSMRRSVYLDNTIEFLRGRVYLGAYDYTPEDTDELVFFTVEDAIFYNSFHLDFGPMNIGHLYRFAVIFHEILNDPENANKAVVFYSSASTRQRANAACMLCCYMILVQAWTPHQVLQPLAQVDPPFMPFRDAGYSNADFEITIQDVVYGVWRAKEKGLIDLHSFNLESYEKYEHVEFGDFNVLTPDFIAFASPQEDHPKGYLATKSSHLNQPFKSVLNFFANNNVQLVVRLNSHLYNKKHFEDIGIQHLDLIFEDGTCPDLSIVKNFVGAAETIIKRGGKIAVHCKAGLGRTGCLIGAHLIYTYGFTANECIGFLRFIRPGMVVGPQQHWLYLHQNDFREWKYTTRISLKPSEAIGGLYPLISLEEYRLQKKKLKD

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	571

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8. Citations (1)

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Unit-cell length a length_a	82.850 Å
Unit-cell length b length_b	95.130 Å
Unit-cell length c length_c	137.760 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	55.791 Å
R factor r_factor	0.1792
R_work r_work	0.1780
R_free r_free	0.2027

fit	/app/data/saxs_computation/xw/5xw4/5xw4.fit
pddf	/app/data/pr_computation/xw/5xw4/5xw4.pr.out
profile	/app/data/saxs_computation/xw/5xw4/5xw4.dat

Crystal structure of budding yeast Cdc14p (wild type) in the apo state

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

Tyrosine-protein phosphatase CDC14

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)