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- PDB-4wh7: Structure of the CDC25B Phosphatase Catalytic Domain with Bound Ligand -

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Basic information

Entry
Database: PDB / ID: 4wh7
TitleStructure of the CDC25B Phosphatase Catalytic Domain with Bound Ligand
ComponentsM-phase inducer phosphatase 2
KeywordsHYDROLASE/HYDROLASE Inhibitor / Phosphatase / Inhibitor / Fragment / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / oocyte maturation / female meiosis I / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of cytokinesis / phosphoprotein phosphatase activity / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of mitotic cell cycle ...positive regulation of G2/MI transition of meiotic cell cycle / oocyte maturation / female meiosis I / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of cytokinesis / phosphoprotein phosphatase activity / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / spindle pole / G2/M transition of mitotic cell cycle / mitotic cell cycle / protein phosphorylation / cell division / centrosome / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
M-phase inducer phosphatase / M-phase inducer phosphatase / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-fluoro-4-hydroxybenzonitrile / M-phase inducer phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLund, G.L. / Dudkin, S. / Borkin, D. / Ni, W. / Grembecka, J. / Cierpicki, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA181185 United States
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Inhibition of CDC25B Phosphatase Through Disruption of Protein-Protein Interaction.
Authors: Lund, G. / Dudkin, S. / Borkin, D. / Ni, W. / Grembecka, J. / Cierpicki, T.
History
DepositionSep 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: M-phase inducer phosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2559
Polymers21,4491
Non-polymers8068
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.207, 71.442, 73.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein M-phase inducer phosphatase 2 / Dual specificity phosphatase Cdc25B


Mass: 21449.424 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 386-565) / Mutation: C473S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC25B, CDC25HU2 / Production host: Escherichia coli (E. coli) / References: UniProt: P30305, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-8H8 / 2-fluoro-4-hydroxybenzonitrile


Mass: 137.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4FNO
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: (NH4)2SO4, Tris, TCEP / PH range: 7.25-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 35426 / % possible obs: 90.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 28.6
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.3 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A2K

2a2k


Resolution: 1.62→36.21 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.743 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19766 1580 5 %RANDOM
Rwork0.15686 ---
obs0.1589 30041 90.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.378 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.62→36.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 46 287 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221611
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.18722180
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31822.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23815273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7031514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211234
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.8731555
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded15.76751509
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 120 -
Rwork0.387 2050 -
obs--88.9 %

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