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- PDB-1ohe: Structure of cdc14b phosphatase with a peptide ligand -

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Basic information

Entry
Database: PDB / ID: 1ohe
TitleStructure of cdc14b phosphatase with a peptide ligand
Components
  • CDC14B2 PHOSPHATASE
  • PEPTIDE LIGAND
KeywordsHYDROLASE / PROTEIN PHOSPHATASE / CELL CYCLE
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / regulation of exit from mitosis / positive regulation of ubiquitin protein ligase activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of cytokinesis / mitotic G2 DNA damage checkpoint signaling / cilium assembly / protein dephosphorylation ...protein tyrosine/serine/threonine phosphatase activity / regulation of exit from mitosis / positive regulation of ubiquitin protein ligase activity / myosin phosphatase activity / protein serine/threonine 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 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A ...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 / Dual specificity protein phosphatase domain profile. / 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)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / Derived calculations ...Data collection / Derived calculations / 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 / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDC14B2 PHOSPHATASE
B: PEPTIDE LIGAND


Theoretical massNumber of molelcules
Total (without water)40,8402
Polymers40,8402
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.760, 53.150, 64.170
Angle α, β, γ (deg.)90.00, 117.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CDC14B2 PHOSPHATASE / CDC14B


Mass: 40461.047 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: Protein/peptide PEPTIDE LIGAND


Mass: 379.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SUBSTRATE / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 30% PEG 8000, 0.1 M ZINC ACETATE PH 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: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 16051 / % possible obs: 97.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.9 / % possible all: 92.2
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 17049 / Num. measured all: 62805 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 92.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1404031 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 998 5.9 %RANDOM
Rwork0.207 ---
obs0.207 17049 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.266 Å2 / ksol: 0.345209 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.64 Å20 Å22.67 Å2
2--12.86 Å20 Å2
3----7.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 0 143 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 154 5.7 %
Rwork0.263 2537 -
obs--92.4 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Refinement
*PLUS
Highest resolution: 2.2 Å / Num. reflection Rfree: 99 / % reflection Rfree: 5.7 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.45

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