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- PDB-5xw4: Crystal structure of budding yeast Cdc14p (wild type) in the apo state -

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Basic information

Entry
Database: PDB / ID: 5xw4
TitleCrystal structure of budding yeast Cdc14p (wild type) in the apo state
ComponentsTyrosine-protein phosphatase CDC14
KeywordsCELL CYCLE / phosphatase
Function / homology
Function and homology information


RENT complex / new mitotic spindle pole body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring assembly / meiotic spindle disassembly / meiotic nuclear division / mitotic spindle pole body / rDNA chromatin condensation / positive regulation of autophagosome assembly / regulation of exit from mitosis ...RENT complex / new mitotic spindle pole body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring assembly / meiotic spindle disassembly / meiotic nuclear division / mitotic spindle pole body / rDNA chromatin condensation / positive regulation of autophagosome assembly / regulation of exit from mitosis / cellular bud neck / autophagy of mitochondrion / rDNA heterochromatin formation / spindle pole body / cellular response to osmotic stress / negative regulation of transcription by RNA polymerase I / positive regulation of cytokinesis / MAPK6/MAPK4 signaling / protein serine/threonine phosphatase activity / phosphoprotein phosphatase activity / protein-tyrosine-phosphatase / positive regulation of autophagy / protein tyrosine phosphatase activity / chromosome segregation / microtubule cytoskeleton organization / spindle pole / mitotic spindle / mitotic cell cycle / cell division / nucleolus / nucleus / cytoplasm
Similarity search - Function
Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / : / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein-tyrosine phosphatase, catalytic ...Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / : / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
Tyrosine-protein phosphatase CDC14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsKobayashi, J. / Matsuura, Y.
CitationJournal: Protein Sci. / Year: 2017
Title: Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae
Authors: Kobayashi, J. / Matsuura, Y.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase CDC14
B: Tyrosine-protein phosphatase CDC14


Theoretical massNumber of molelcules
Total (without water)95,2822
Polymers95,2822
Non-polymers00
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-11 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.850, 95.130, 137.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein phosphatase CDC14


Mass: 47640.832 Da / Num. of mol.: 2 / Fragment: UNP residues 1-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CDC14, OAF3, YFR028C / Production host: Escherichia coli (E. coli) / References: UniProt: Q00684, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Bis-Tris, ammonium sulfate, PEG4000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→55.791 Å / Num. obs: 91638 / % possible obs: 98.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.884.20.6160.7440.3370.70682.2
10.13-55.795.70.0360.9980.0160.03998.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHE

1ohe


Resolution: 1.85→55.791 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.45
RfactorNum. reflection% reflection
Rfree0.2027 4571 4.99 %
Rwork0.178 --
obs0.1792 91545 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.57 Å2 / Biso mean: 32.2884 Å2 / Biso min: 12.54 Å2
Refinement stepCycle: final / Resolution: 1.85→55.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 0 571 6526
Biso mean---38.08 -
Num. residues----737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046125
X-RAY DIFFRACTIONf_angle_d0.6658320
X-RAY DIFFRACTIONf_chiral_restr0.046887
X-RAY DIFFRACTIONf_plane_restr0.0051082
X-RAY DIFFRACTIONf_dihedral_angle_d2.873556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8710.32731120.27322388250081
1.871-1.89310.27451250.26332477260285
1.8931-1.91610.28471320.24382606273889
1.9161-1.94040.25581310.23212691282292
1.9404-1.96590.25521400.23112806294696
1.9659-1.99290.23811560.21932840299697
1.9929-2.02130.241500.222629153065100
2.0213-2.05150.26041760.210128973073100
2.0515-2.08360.26051510.213629433094100
2.0836-2.11770.24081540.200129533107100
2.1177-2.15420.24581480.194729173065100
2.1542-2.19340.22471680.18529153083100
2.1934-2.23560.20821490.180529443093100
2.2356-2.28120.1961440.184429543098100
2.2812-2.33080.21641570.184129593116100
2.3308-2.38510.21221540.184429163070100
2.3851-2.44470.2031540.183329513105100
2.4447-2.51080.22561620.173229533115100
2.5108-2.58470.22021690.17929353104100
2.5847-2.66810.18011440.165729533097100
2.6681-2.76350.20591360.179729783114100
2.7635-2.87410.2311720.178529673139100
2.8741-3.00490.20141570.17529493106100
3.0049-3.16330.20251790.180529693148100
3.1633-3.36150.19591510.174329483099100
3.3615-3.6210.20621330.167530133146100
3.621-3.98530.1751610.153530193180100
3.9853-4.56180.15951740.140329943168100
4.5618-5.74640.16781550.160430693224100
5.7464-55.81620.19251770.1983155333299

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