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- PDB-1ohc: Structure of the proline directed phosphatase cdc14 -

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Basic information

Entry
Database: PDB / ID: 1ohc
TitleStructure of the proline directed phosphatase cdc14
ComponentsCDC14B2 PHOSPHATASE
KeywordsHYDROLASE / DUAL SPECIFICITY PHOSPHATASE
Function / homology
Function and homology information


regulation of exit from mitosis / positive regulation of ubiquitin protein ligase activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of cytokinesis / mitotic G2 DNA damage checkpoint signaling / cilium assembly / protein dephosphorylation / protein-tyrosine-phosphatase ...regulation of exit from mitosis / positive regulation of ubiquitin protein ligase activity / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of cytokinesis / mitotic G2 DNA damage checkpoint signaling / cilium assembly / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / MAPK6/MAPK4 signaling / mitotic spindle / microtubule cytoskeleton organization / spindle pole / DNA repair / centrosome / nucleolus / nucleoplasm / 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 / : / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily ...Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / : / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase CDC14B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsGray, C.H. / Good, V.M. / Tonks, N.K. / Barford, D.
CitationJournal: Embo J. / Year: 2003
Title: The Structure of the Cell Cycle Protein Cdc14 Reveals a Proline-Directed Protein Phosphatase
Authors: Gray, C.H. / Good, V.M. / Tonks, N.K. / Barford, D.
History
DepositionMay 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDC14B2 PHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)40,4771
Polymers40,4771
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.702, 51.937, 65.070
Angle α, β, γ (deg.)90.00, 118.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CDC14B2 PHOSPHATASE / CDC14B


Mass: 40477.109 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN, RESIDUES 39-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O60729
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.6 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS ACETATE, 30% PEG 8000PH 8.0, 20 OC HANGING DROP VAPOUR DIFFUSION
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
2100 mMTris-acetate1reservoirpH8.0
330 %PEG40001reservoir
40.2 M1reservoirMgCl2
57 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 11713 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.345 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.2 % / Num. measured all: 38931 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.345

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→40.51 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1798734.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 589 5.2 %RANDOM
Rwork0.201 ---
obs0.201 11403 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.3452 Å2 / ksol: 0.331709 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å24.7 Å2
2--13.68 Å20 Å2
3----11.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 0 57 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 100 5.4 %
Rwork0.282 1745 -
obs--95.4 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Refinement
*PLUS
Highest resolution: 2.5 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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