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- PDB-7zmx: Crystal structure of the Plant Homeodomain (PHD) of human ING3 -

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Basic information

Entry
Database: PDB / ID: 7zmx
TitleCrystal structure of the Plant Homeodomain (PHD) of human ING3
ComponentsInhibitor of growth protein 3
KeywordsNUCLEAR PROTEIN / ING3 / PHD / histone binding / human / nuclear
Function / homology
Function and homology information


piccolo histone acetyltransferase complex / histone H4K12 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / Rpd3L complex / histone H4K16 acetyltransferase activity / Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination ...piccolo histone acetyltransferase complex / histone H4K12 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / Rpd3L complex / histone H4K16 acetyltransferase activity / Swr1 complex / regulation of double-strand break repair / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / nucleosome / HATs acetylate histones / regulation of apoptotic process / regulation of cell cycle / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
ING3, PHD domain / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type ...ING3, PHD domain / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Inhibitor of growth protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFerreras, M.O. / Medrano, F.J. / Blanco, F.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-113225GB-I00 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural analysis of ING3 protein and histone H3 binding.
Authors: Ferreras-Gutierrez, M. / Chaves-Arquero, B. / Gonzalez-Magana, A. / Merino, N. / Amusategui-Mateu, I. / Huecas, S. / Medrano, F.J. / Blanco, F.J.
History
DepositionApr 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 24, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 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: Inhibitor of growth protein 3
B: Inhibitor of growth protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3039
Polymers12,9212
Non-polymers3827
Water1,76598
1
A: Inhibitor of growth protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6314
Polymers6,4601
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inhibitor of growth protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6715
Polymers6,4601
Non-polymers2114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.695, 40.695, 100.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

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Components

#1: Protein Inhibitor of growth protein 3 / p47ING3


Mass: 6460.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GAMG are non-native / Source: (gene. exp.) Homo sapiens (human) / Gene: ING3, HSPC301 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NXR8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.86 Å3/Da / Density % sol: 33.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: Protein solution: ING3 PHD at 20 mg/ml in Tris 20 mM pH = 6.5, 150 mM NaCl, 1 mM DTT. Reservoir solution: 0.1 M Tris pH = 8.4, 30% PEG 4000, 0.2 M calcium chloride Mixture of 1 ul of protein ...Details: Protein solution: ING3 PHD at 20 mg/ml in Tris 20 mM pH = 6.5, 150 mM NaCl, 1 mM DTT. Reservoir solution: 0.1 M Tris pH = 8.4, 30% PEG 4000, 0.2 M calcium chloride Mixture of 1 ul of protein solution with 1 ul of reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.2→35.24 Å / Num. obs: 47743 / % possible obs: 92.4 % / Redundancy: 14.8 % / Biso Wilson estimate: 18.28 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.032 / Rrim(I) all: 0.094 / Net I/σ(I): 18.59
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 0.18 / Num. unique obs: 51 / CC1/2: 0.76 / Rpim(I) all: 0.414 / Rrim(I) all: 0.723 / % possible all: 45.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vnf

2vnf


Resolution: 1.2→35.24 Å / SU ML: 0.1549 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 3381 7.08 %
Rwork0.172 44362 -
obs0.1743 47743 82.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.89 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 7 98 934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091854
X-RAY DIFFRACTIONf_angle_d0.99881158
X-RAY DIFFRACTIONf_chiral_restr0.0793112
X-RAY DIFFRACTIONf_plane_restr0.0093151
X-RAY DIFFRACTIONf_dihedral_angle_d9.579113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.802370.440446X-RAY DIFFRACTION2.18
1.22-1.240.329690.4608157X-RAY DIFFRACTION6.92
1.24-1.260.4337300.4038398X-RAY DIFFRACTION18.22
1.26-1.280.4168610.3769689X-RAY DIFFRACTION29.8
1.28-1.30.3207940.35791140X-RAY DIFFRACTION53.03
1.3-1.320.32511450.31041704X-RAY DIFFRACTION75.25
1.32-1.350.30661470.30161996X-RAY DIFFRACTION88.37
1.35-1.370.31691660.28542228X-RAY DIFFRACTION97.83
1.38-1.40.26911680.24922255X-RAY DIFFRACTION100
1.41-1.440.29261670.22742230X-RAY DIFFRACTION100
1.44-1.470.21631660.21572236X-RAY DIFFRACTION100
1.47-1.510.22611720.19932262X-RAY DIFFRACTION100
1.51-1.560.26171700.19322262X-RAY DIFFRACTION100
1.56-1.610.25841740.16582237X-RAY DIFFRACTION99.96
1.61-1.670.17381780.16042242X-RAY DIFFRACTION100
1.67-1.730.171570.15782263X-RAY DIFFRACTION100
1.73-1.810.19111700.15042254X-RAY DIFFRACTION99.92
1.81-1.910.19681820.1762250X-RAY DIFFRACTION100
1.91-2.030.15911720.16462252X-RAY DIFFRACTION100
2.03-2.180.19811660.15672228X-RAY DIFFRACTION99.92
2.18-2.40.20421620.16622308X-RAY DIFFRACTION100
2.4-2.750.17471550.17392237X-RAY DIFFRACTION99.96
2.75-3.460.18051840.15942229X-RAY DIFFRACTION100
3.46-35.240.21981790.15652259X-RAY DIFFRACTION99.92

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