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

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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 / homologyCyclin-dependent kinase inhibitor 3 (CDKN3) / un:q16667:
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 2000 / Release: May 9, 2001
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 9, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Mar 14, 2018Structure modelDatabase referencesstruct_ref_seq_dif_struct_ref_seq_dif.details

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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
Polyers142,9146
Non-polymers5766
Water12,430690
1
A: CYCLIN-DEPENDENT KINASE INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9152
Polyers23,8191
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
Polyers23,8191
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
Polyers23,8191
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
Polyers23,8191
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
Polyers23,8191
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
Polyers23,8191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 65

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Components

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


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


Mass: 96.063 Da / Num. of mol.: 6 / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / Formula: H2O / Water

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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 / Density percent sol: 50.09 %
Crystal growTemp: 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
Temp: 4 ℃ / Details: Hanlon, N., (1998) Protein Sci., 7, 508.
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC / Detector: CCD / Collection date: Jan 1, 2000
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 23.6 Å2 / D resolution high: 2 Å / D resolution low: 5 Å / Number obs: 90055 / Observed criterion sigma F: 2 / Observed criterion sigma I: 2 / Rmerge I obs: 0.06 / NetI over sigmaI: 9.3 / Redundancy: 3.6 % / Percent possible obs: 96.7
Reflection shellRmerge I obs: 0.38 / Highest resolution: 2 Å / Lowest resolution: 2.12 Å / Percent possible all: 91.6
Reflection
*PLUS
Number measured all: 319770
Reflection shell
*PLUS
Percent possible obs: 91.6 / MeanI over sigI obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefineR Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.253 / R factor R work: 0.202 / Highest resolution: 2 Å / Lowest resolution: 2 Å / Number reflection R free: 4241 / Number reflection obs: 88032 / Percent reflection obs: 96.7
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 8340 / Nucleic acid: 0 / Ligand: 30 / Solvent: 690 / Total: 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
Refine
*PLUS
Sigma F: 0
Least-squares process
*PLUS
R factor obs: 0.202 / Highest resolution: 2 Å / Lowest resolution: 2 Å / Percent reflection R free: 1

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