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- PDB-5xfo: Structure of the N-terminal domains of PHF1 -

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Basic information

Entry
Database: PDB / ID: 5xfo
TitleStructure of the N-terminal domains of PHF1
ComponentsPHD finger protein 1
KeywordsTRANSCRIPTION / PHF1 / PCL1 / PRC2
Function / homology
Function and homology information


histone methyltransferase binding / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / site of double-strand break / centrosome / chromatin binding / DNA binding ...histone methyltransferase binding / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / site of double-strand break / centrosome / chromatin binding / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
PHD finger protein 1 / : / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...PHD finger protein 1 / : / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHD finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWang, Z. / Li, H.
CitationJournal: Nature / Year: 2017
Title: Polycomb-like proteins link the PRC2 complex to CpG islands
Authors: Li, H. / Liefke, R. / Jiang, J. / Kurland, J.V. / Tian, W. / Deng, P. / Zhang, W. / He, Q. / Patel, D.J. / Bulyk, M.L. / Shi, Y. / Wang, Z.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2235
Polymers35,9621
Non-polymers2624
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.467, 66.772, 76.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHD finger protein 1 / hPHF1 / Polycomb-like protein 1 / hPCl1


Mass: 35961.672 Da / Num. of mol.: 1 / Fragment: UNP residues 25-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF1, PCL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43189
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-pH 8.0, 10% PEG 3350, 22% ethylene glycerol

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→29.34 Å / Num. obs: 25789 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1262 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.338 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.2271 1308 5.08 %
Rwork0.1772 --
obs0.1797 25732 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 4 203 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072574
X-RAY DIFFRACTIONf_angle_d1.0363477
X-RAY DIFFRACTIONf_dihedral_angle_d14.061968
X-RAY DIFFRACTIONf_chiral_restr0.044362
X-RAY DIFFRACTIONf_plane_restr0.005448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8857-1.96120.29111310.20912515X-RAY DIFFRACTION94
1.9612-2.05040.22161630.18632677X-RAY DIFFRACTION100
2.0504-2.15850.24581330.16862717X-RAY DIFFRACTION100
2.1585-2.29370.25021470.17792681X-RAY DIFFRACTION100
2.2937-2.47070.23221560.17442707X-RAY DIFFRACTION100
2.4707-2.71920.2141400.17582714X-RAY DIFFRACTION100
2.7192-3.11230.24261460.17612740X-RAY DIFFRACTION100
3.1123-3.91960.2191510.17012768X-RAY DIFFRACTION100
3.9196-29.34130.20541410.17912905X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.0901 Å / Origin y: -1.5861 Å / Origin z: -8.012 Å
111213212223313233
T0.0775 Å2-0.0097 Å2-0.0073 Å2-0.067 Å20.0193 Å2--0.0611 Å2
L0.309 °20.1055 °20.0287 °2-0.3521 °20.0328 °2--0.317 °2
S-0.0672 Å °-0.0039 Å °0.022 Å °0.0276 Å °0.0234 Å °-0.0099 Å °-0.0793 Å °-0.0233 Å °-0.0015 Å °
Refinement TLS groupSelection details: all

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