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- PDB-1fpz: CRYSTAL STRUCTURE ANALYSIS OF KINASE ASSOCIATED PHOSPHATASE (KAP)... -

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Basic information

Entry
Database: PDB / ID: 1fpz
TitleCRYSTAL STRUCTURE ANALYSIS OF KINASE ASSOCIATED PHOSPHATASE (KAP) WITH A SUBSTITUTION OF THE CATALYTIC SITE CYSTEINE (CYS140) TO A SERINE
ComponentsCYCLIN-DEPENDENT KINASE INHIBITOR 3Cyclin-dependent kinase inhibitor protein
KeywordsHYDROLASE / alpha-beta sandwich
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / regulation of cyclin-dependent protein serine/threonine kinase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / G1/S transition of mitotic cell cycle / regulation of cell cycle ...protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / regulation of cyclin-dependent protein serine/threonine kinase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / G1/S transition of mitotic cell cycle / regulation of cell cycle / negative regulation of cell population proliferation / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin-dependent kinase inhibitor 3 / CDKN3 domain / Cyclin-dependent kinase inhibitor 3 (CDKN3) / 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 domain ...Cyclin-dependent kinase inhibitor 3 / CDKN3 domain / Cyclin-dependent kinase inhibitor 3 (CDKN3) / 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 domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cyclin-dependent kinase inhibitor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSong, H. / Hanlon, N. / Brown, N.R. / Noble, M.E.M. / Johnson, L.N. / Barford, D.
Citation
Journal: Mol.Cell / Year: 2001
Title: Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2.
Authors: Song, H. / Hanlon, N. / Brown, N.R. / Noble, M.E. / Johnson, L.N. / Barford, D.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2
Authors: Gyruris, J. / Golemis, E. / Chertkov, H. / Brent, R.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: The p21Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases
Authors: Harper, J.W. / Adami, G.R. / Wei, N. / Keyomarsi, K. / Elledge, S.J.
History
DepositionSep 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CYCLIN-DEPENDENT KINASE INHIBITOR 3
B: CYCLIN-DEPENDENT KINASE INHIBITOR 3
C: CYCLIN-DEPENDENT KINASE INHIBITOR 3
D: CYCLIN-DEPENDENT KINASE INHIBITOR 3
E: CYCLIN-DEPENDENT KINASE INHIBITOR 3
F: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,49112
Polymers142,9146
Non-polymers5766
Water12,430690
1
A: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9152
Polymers23,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9152
Polymers23,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9152
Polymers23,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9152
Polymers23,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9152
Polymers23,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9152
Polymers23,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.930, 131.930, 140.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
CYCLIN-DEPENDENT KINASE INHIBITOR 3 / Cyclin-dependent kinase inhibitor protein


Mass: 23819.057 Da / Num. of mol.: 6 / Mutation: C140S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: Q16667, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, ammonium sulphate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Hanlon, N., (1998) Protein Sci., 7, 508.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
224 %(w/v)PEG80001reservoir
30.1 Msodium acetate1reservoir
40.4 Mammonium sulfate1reservoir
51 mMphosphopeptide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 90055 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.12 Å / Rmerge(I) obs: 0.38 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 319770
Reflection shell
*PLUS
% possible obs: 91.6 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4241 -RANDOM
Rwork0.202 ---
obs-88032 96.7 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8340 0 30 690 9060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_bond_d0.012
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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