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- PDB-2qic: Crystal Structure of the ING1 PHD Finger in complex with a Histon... -

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Basic information

Entry
Database: PDB / ID: 2qic
TitleCrystal Structure of the ING1 PHD Finger in complex with a Histone H3K4ME3 peptide
Components
  • H3K4ME3 PEPTIDE
  • Inhibitor of growth protein 1
KeywordsANTITUMOR PROTEIN / APOPTOSIS / PHD / ING1 / HISTONE / H3K4ME3 / CHROMATIN
Function / homologyZinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth protein 1 / Inhibitor of growth protein, N-terminal histone-binding / Zinc finger, PHD-finger / Zinc finger, PHD-type, conserved site / Zinc finger, PHD-type / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth protein 1 / Inhibitor of growth protein, N-terminal histone-binding / Zinc finger, PHD-finger / Zinc finger, PHD-type, conserved site / Zinc finger, PHD-type / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / regulation of cell death / methylated histone binding / negative regulation of cell growth / cell cycle / negative regulation of cell population proliferation / positive regulation of transcription, DNA-templated / metal ion binding / nucleus / Inhibitor of growth protein 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / 2.1 Å resolution
AuthorsPena, P.V. / Champagne, K. / Zhao, R. / Kutateladze, T.G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.
Authors: Pena, P.V. / Hom, R.A. / Hung, T. / Lin, H. / Kuo, A.J. / Wong, R.P. / Subach, O.M. / Champagne, K.S. / Zhao, R. / Verkhusha, V.V. / Li, G. / Gozani, O. / Kutateladze, T.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2007 / Release: May 13, 2008
RevisionDateData content typeGroupProviderType
1.0May 13, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

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Assembly

Deposited unit
A: Inhibitor of growth protein 1
B: H3K4ME3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5574
Polyers8,4262
Non-polymers1312
Water73941
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Inhibitor of growth protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2073
Polyers7,0761
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: H3K4ME3 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)1,3511
Polyers1,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)49.060, 49.060, 52.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP 32 2 1

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Components

#1: Protein/peptide Inhibitor of growth protein 1


Mass: 7075.926 Da / Num. of mol.: 1 / Fragment: PHD DOMAIN (RESIDUES 345-404) / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Gene: ING1 / Plasmid name: PGEX-2T / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9UK53
#2: Protein/peptide H3K4ME3 PEPTIDE


Mass: 1350.568 Da / Num. of mol.: 1 / Details: Synthetic PEPTIDE H3K4ME3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.17 / Density percent sol: 43.26 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.01 M NiCl2 6H20, 0.1 M Tris, 20% polyethylene glycol monomethyl ether 2K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.257 Å
DetectorDetector: AREA DETECTOR / Collection date: Feb 26, 2007
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.257 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 25 Å / Number all: 4526 / Number obs: 4526 / Observed criterion sigma F: 0 / Rmerge I obs: 0.071 / NetI over sigmaI: 16.3 / Redundancy: 9.35 % / Percent possible obs: 100
Reflection shellRmerge I obs: 0.253 / Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / MeanI over sigI obs: 5.4 / Number unique all: 450 / Redundancy: 9.78 % / Percent possible all: 100

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Processing

Software
NameClassification
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefineMethod to determine structure: Rigid Body Refinement
Starting model: PDB entry 2G6Q
R Free selection details: RANDOM
Least-squares processR factor R free: 0.264 / R factor R work: 0.24 / Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Number reflection R free: 473 / Number reflection all: 4526 / Number reflection obs: 4526 / Percent reflection obs: 99.9
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 25 Å
Number of atoms included #LASTProtein: 477 / Nucleic acid: 0 / Ligand: 2 / Solvent: 41 / Total: 520
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.091
Refine LS shellHighest resolution: 2.1 Å / R factor R free: 0.33 / R factor R work: 0.281 / Lowest resolution: 2.18 Å / Number reflection R free: 62 / Number reflection obs: 448 / Percent reflection obs: 100

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