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- PDB-1mx6: Structure of p18INK4c (F92N) -

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Basic information

Entry
Database: PDB / ID: 1mx6
TitleStructure of p18INK4c (F92N)
ComponentsCyclin-dependent kinase 6 inhibitor
Keywordscell cycle inhibitor / Ankyrin repeats
Function / homology
Function and homology information


negative regulation of phosphorylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / oligodendrocyte differentiation / regulation of G1/S transition of mitotic cell cycle / negative regulation of stem cell proliferation / stem cell proliferation / negative regulation of cell growth / Oncogene Induced Senescence / Cyclin D associated events in G1 ...negative regulation of phosphorylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / oligodendrocyte differentiation / regulation of G1/S transition of mitotic cell cycle / negative regulation of stem cell proliferation / stem cell proliferation / negative regulation of cell growth / Oncogene Induced Senescence / Cyclin D associated events in G1 / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / negative regulation of cell population proliferation / protein kinase binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily ...: / Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Cyclin-dependent kinase 4 inhibitor C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMarmorstein, R. / Venkataramani, R.N. / MacLachlan, T.K. / Chai, X. / El-Deiry, W.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure-based design of p18INK4c proteins with increased thermodynamic stability and cell cycle inhibitory activity
Authors: Venkataramani, R.N. / MacLachlan, T.K. / Chai, X. / El-Deiry, W.S. / Marmorstein, R.
History
DepositionOct 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 6 inhibitor
B: Cyclin-dependent kinase 6 inhibitor


Theoretical massNumber of molelcules
Total (without water)36,2332
Polymers36,2332
Non-polymers00
Water3,135174
1
A: Cyclin-dependent kinase 6 inhibitor


Theoretical massNumber of molelcules
Total (without water)18,1161
Polymers18,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-dependent kinase 6 inhibitor


Theoretical massNumber of molelcules
Total (without water)18,1161
Polymers18,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.005, 150.843, 40.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cyclin-dependent kinase 6 inhibitor / p18-INK6 / Cyclin-dependent kinase 4 inhibitor C / p18-INK4c


Mass: 18116.285 Da / Num. of mol.: 2 / Mutation: F92N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42773
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5 mg/ml protein, 20 mM Tris (pH 8.5), 0.5 mM DTT, 14 % PEG 6000 and 2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMTris1droppH8.5
30.5 mMdithiothreitol1drop
47 %PEG60001drop
51 M1dropNaCl
614 %PEG60001reservoir
72 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 23674 / Num. obs: 22869 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.496 / % possible all: 91.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IHB

1ihb


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2287 -random
Rwork0.237 ---
all0.24 23674 --
obs0.24 22869 96.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.167 Å20 Å20 Å2
2--7.63 Å20 Å2
3----2.463 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 0 174 2549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_bond_d0.006
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS

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