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- PDB-2uzq: Protein Phosphatase, New Crystal Form -

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Basic information

Entry
Database: PDB / ID: 2uzq
TitleProtein Phosphatase, New Crystal Form
ComponentsM-PHASE INDUCER PHOSPHATASE 2
KeywordsHYDROLASE / CELL DIVISION / PHOSPHORYLATION / DUAL SPECIFICITY / MITOSIS / CELL CYCLE / PHOSPHATASE / PROTEIN PHOSPHATASE
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 / cell division / protein phosphorylation / 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
PHOSPHATE ION / M-phase inducer phosphatase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHillig, R.C. / Eberspaecher, U.
Citation
Journal: To be Published
Title: New Crystal Form of Protein Phosphatase Cdc25B Triggered by Guanidinium Chloride as an Additive
Authors: Hillig, R.C. / Eberspaecher, U.
#1: Journal: Biochemistry / Year: 2005
Title: Experimental Validation of the Docking Orientation of Cdc25 with its Cdk2-Cyca Protein Substrate.
Authors: Sohn, J. / Parks, J.M. / Buhrman, G. / Brown, P. / Kristjansdottir, K. / Safi, A. / Edelsbrunner, H. / Yang, W. / Rudolph, J.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of the Catalytic Subunit of Cdc25B Required for G2/M Phase Transition of the Cell Cycle.
Authors: Reynolds, R.A. / Yem, A.W. / Wolfe, C.L. / Deibel, M.R.J. / Chidester, C.G. / Watenpaugh, K.D.
History
DepositionMay 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: M-PHASE INDUCER PHOSPHATASE 2
B: M-PHASE INDUCER PHOSPHATASE 2
C: M-PHASE INDUCER PHOSPHATASE 2
D: M-PHASE INDUCER PHOSPHATASE 2
E: M-PHASE INDUCER PHOSPHATASE 2
F: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,27512
Polymers140,7056
Non-polymers5706
Water3,531196
1
A: M-PHASE INDUCER PHOSPHATASE 2
B: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0924
Polymers46,9022
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5.6 kcal/mol
Surface area20460 Å2
MethodPQS
2
C: M-PHASE INDUCER PHOSPHATASE 2
D: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0924
Polymers46,9022
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-7.4 kcal/mol
Surface area20280 Å2
MethodPQS
3
E: M-PHASE INDUCER PHOSPHATASE 2
F: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0924
Polymers46,9022
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7.2 kcal/mol
Surface area20420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)123.925, 123.925, 174.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99922, -0.00332, -0.03927), (0.00389, -0.99989, -0.01446), (-0.03921, -0.0146, 0.99912)63.3389, 176.33797, 2.37184
2given(0.5764, -0.8167, 0.02771), (0.81614, 0.57705, 0.03061), (-0.04098, 0.00497, 0.99915)54.98053, -41.32238, 22.6779
3given(-0.58725, 0.8094, 0.00139), (-0.80845, -0.58647, -0.04959), (-0.03932, -0.03025, 0.99877)-51.85634, 112.94102, 25.71187
4given(0.98738, 0.07916, 0.13718), (-0.0887, 0.99395, 0.06484), (-0.13122, -0.07619, 0.98842)-69.33879, -31.47198, 6.67416
5given(-0.99493, -0.04044, 0.09203), (0.0453, -0.99765, 0.05132), (0.08974, 0.05523, 0.99443)3.75284, 140.10407, -11.50927

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Components

#1: Protein
M-PHASE INDUCER PHOSPHATASE 2 / DUAL SPECIFICITY PHOSPHATASE CDC25B / CDC25B


Mass: 23450.812 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 377-566
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30305, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONTAINS N-TERMINAL RESIDUES WHICH REPRESENT A CLONING ARTIFACT (THROMBIN CLEAVAGE SITE ...SEQUENCE CONTAINS N-TERMINAL RESIDUES WHICH REPRESENT A CLONING ARTIFACT (THROMBIN CLEAVAGE SITE AND POLY GLY LINKER, GSPGIS GGGGG). OUT OF THE FOUR ISOFORM SEQUENCES GENERATED BY ALTERNATE SPLICING, THE ENTRY BELONGS TO ISOFORM 1

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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: 2.7 Å3/Da / Density % sol: 53.4 %
Crystal growpH: 7 / Details: PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95368
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 2.38→36.8 Å / Num. obs: 58835 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / % possible all: 89.3

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Processing

Software
NameVersionClassification
CNX2002refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QB0

1qb0


Resolution: 2.38→36.77 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3108 5.3 %RANDOM
Rwork0.226 ---
obs-58824 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1889 Å2 / ksol: 0.355341 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å29.68 Å20 Å2
2--2.95 Å20 Å2
3----5.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.38→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8472 0 30 196 8698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.42
X-RAY DIFFRACTIONc_mcangle_it2.413
X-RAY DIFFRACTIONc_scbond_it1.94.5
X-RAY DIFFRACTIONc_scangle_it2.926
Refine LS restraints NCSNCS model details: NCS RESTRAINTS
LS refinement shellResolution: 2.38→2.47 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.34 4.7 %
Rwork0.308 -
obs-88.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: ION.TOP

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