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- PDB-1ihb: CRYSTAL STRUCTURE OF P18-INK4C(INK6) -

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Basic information

Entry
Database: PDB / ID: 1ihb
TitleCRYSTAL STRUCTURE OF P18-INK4C(INK6)
ComponentsCYCLIN-DEPENDENT KINASE 6 INHIBITOR
KeywordsCELL CYCLE INHIBITOR / P18-INK4C(INK6) / ANKYRIN REPEAT / CDK 4/6 INHIBITOR
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 / MIR / Resolution: 1.95 Å
AuthorsRavichandran, V. / Swaminathan, K. / Marmorstein, R.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of the CDK4/6 inhibitory protein p18INK4c provides insights into ankyrin-like repeat structure/function and tumor-derived p16INK4 mutations.
Authors: Venkataramani, R. / Swaminathan, K. / Marmorstein, R.
History
DepositionOct 25, 1997Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,1292
Polymers35,1292
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.510, 151.700, 40.460
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-INK4C(INK6)


Mass: 17564.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: P18-INK4C(INK6) / Plasmid: BL21 / Species (production host): Escherichia coli / Gene (production host): P18-INK4C(INK6) / 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.: 207 / 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: 2.3 Å3/Da / Density % sol: 44.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: VAPOR DIFFUSION, 4 DEG. C, 2 MICROLITER HANGING DROP CONTAINING 5 MG/ML PROTEIN, 20 MM TRIS (PH 8.5), 25 MM (NH4)2 HPO4, 0.5 MM DDT, 7% PEG 6K, 1 MM NACL EQUILIBRATED OVER A RESERVOIR ...Details: VAPOR DIFFUSION, 4 DEG. C, 2 MICROLITER HANGING DROP CONTAINING 5 MG/ML PROTEIN, 20 MM TRIS (PH 8.5), 25 MM (NH4)2 HPO4, 0.5 MM DDT, 7% PEG 6K, 1 MM NACL EQUILIBRATED OVER A RESERVOIR CONTAINING 14% PEG 6K AND 2 M NACL. WITHIN 8 DAYS, 0.2 X 0.2 X 0.4 MM CRYSTALS., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1drop
325 mM1dropNH42HPO4
40.5 mMdithiothreitol1drop
57 %PEG60001drop
61 M1dropNaCl
714 %PEG60001reservoir
82 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 1996 / Details: MSC/YALE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 24019 / % possible obs: 90.3 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.049
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 95 % / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
RefinementMethod to determine structure: MIR / Resolution: 1.95→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2208 9.9 %RANDOM
Rwork0.209 ---
obs0.209 22215 87.6 %-
Displacement parametersBiso mean: 18.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 0 207 2590
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.48
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.891.5
X-RAY DIFFRACTIONx_mcangle_it2.722
X-RAY DIFFRACTIONx_scbond_it3.692
X-RAY DIFFRACTIONx_scangle_it5.582.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 200 8.9 %
Rwork0.265 2048 -
obs--54.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 3 / Rfactor all: 0.211 / Rfactor obs: 0.205 / Rfactor Rfree: 0.284
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.48
LS refinement shell
*PLUS
Rfactor obs: 0.265

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