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- PDB-3op3: Crystal Structure of Cell Division Cycle 25C Protein Isoform A fr... -

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Basic information

Entry
Database: PDB / ID: 3op3
TitleCrystal Structure of Cell Division Cycle 25C Protein Isoform A from Homo sapiens
ComponentsM-phase inducer phosphatase 3
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / alpha-beta-alpha sandwich / kinase / cytosol
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / WW domain binding / Polo-like kinase mediated events / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of mitotic nuclear division / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of cyclin-dependent protein serine/threonine kinase activity / phosphoprotein phosphatase activity / Activation of ATR in response to replication stress / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...positive regulation of G2/MI transition of meiotic cell cycle / WW domain binding / Polo-like kinase mediated events / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of mitotic nuclear division / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of cyclin-dependent protein serine/threonine kinase activity / phosphoprotein phosphatase activity / Activation of ATR in response to replication stress / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / RHO GTPases activate PKNs / positive regulation of G2/M transition of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitochondrial intermembrane space / G2/M transition of mitotic cell cycle / spermatogenesis / cell population proliferation / cell division / protein kinase binding / perinuclear region of cytoplasm / 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
M-phase inducer phosphatase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsKim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. ...Kim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / von Delft, F. / Knapp, S. / Joachimiak, A. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Cell Division Cycle 25C Protein Isoform A from Homo sapiens
Authors: Kim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / ...Authors: Kim, Y. / Weger, A. / Hatzos, C. / Savitsky, P. / Johansson, C. / Ball, L. / Barr, A. / Vollmar, M. / Muniz, J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / von Delft, F. / Knapp, S. / Joachimiak, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M-phase inducer phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7925
Polymers25,4081
Non-polymers3844
Water79344
1
A: M-phase inducer phosphatase 3
hetero molecules

A: M-phase inducer phosphatase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,58410
Polymers50,8162
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area2980 Å2
ΔGint-110 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.187, 96.187, 61.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein M-phase inducer phosphatase 3 / Dual specificity phosphatase Cdc25C


Mass: 25407.881 Da / Num. of mol.: 1 / Fragment: UNP residues 270-462
Source method: isolated from a genetically manipulated source
Details: Cleavable N-terminal His6 tag / Source: (gene. exp.) Homo sapiens (human) / Gene: CDC25C / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P30307, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis Tris pH 5.5, 23% PEG 3350, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. all: 9980 / Num. obs: 9980 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 78 Å2 / Rsym value: 0.097 / Net I/σ(I): 7.4
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 437 / Rsym value: 0.759 / % possible all: 87.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
CCP4model building
BALBESphasing
BUSTER2.8.0refinement
REFMACrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 2IFV
Resolution: 2.63→49.31 Å / Cor.coef. Fo:Fc: 0.9391 / Cor.coef. Fo:Fc free: 0.9338 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 474 4.81 %RANDOM
Rwork0.198 ---
all0.199 9851 --
obs0.199 9851 98.4 %-
Displacement parametersBiso mean: 80.16 Å2
Baniso -1Baniso -2Baniso -3
1-7.4335 Å20 Å20 Å2
2--7.4335 Å20 Å2
3----14.867 Å2
Refine analyzeLuzzati coordinate error obs: 0.431 Å
Refinement stepCycle: LAST / Resolution: 2.63→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 20 44 1402
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONf_bond_d0.0114002
X-RAY DIFFRACTIONf_angle_deg1.1119012
X-RAY DIFFRACTIONf_dihedral_angle_d4592
X-RAY DIFFRACTIONf_incorr_chiral_ct
X-RAY DIFFRACTIONf_pseud_angle
X-RAY DIFFRACTIONf_trig_c_planes282
X-RAY DIFFRACTIONf_gen_planes2075
X-RAY DIFFRACTIONf_it140020
X-RAY DIFFRACTIONf_nbd
X-RAY DIFFRACTIONf_omega_torsion2.73
X-RAY DIFFRACTIONf_other_torsion19.28
X-RAY DIFFRACTIONf_improper_torsion
X-RAY DIFFRACTIONf_chiral_improper_torsion1695
X-RAY DIFFRACTIONf_sum_occupancies
X-RAY DIFFRACTIONf_utility_distance
X-RAY DIFFRACTIONf_utility_angle
X-RAY DIFFRACTIONf_utility_torsion
X-RAY DIFFRACTIONf_ideal_dist_contact15774
LS refinement shellResolution: 2.63→2.94 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2873 137 5.17 %
Rwork0.2164 2515 -
all0.2199 2652 -
obs-2652 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.9454-0.52633.44453.3646-1.3723.71380.277-0.6985-0.74350.06450.26720.19920.1852-0.47-0.5442-0.2936-0.09090.069-0.02020.18450.304-11.376140.339-3.9855
2-1.6841.23811.92393.02510.922100.0027-0.00460.01760.00270.04170.0360.03330.0564-0.04440.0398-0.0743-0.1162-0.2254-0.10270.304-12.167841.9405-18.4435
34.25050.94773.23771.50930.21293.26670.1607-0.1696-0.4259-0.26960.24820.38250.5110.018-0.4089-0.2652-0.0536-0.0816-0.23470.07820.304-7.263737.2625-7.1397
410.378-0.66210.0644.4213-0.06690.19790.1094-0.0253-0.7435-0.33120.20240.1992-0.3705-0.3127-0.3119-0.25-0.0824-0.0039-0.1806-0.0390.1677-22.359650.7113-18.9812

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