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- PDB-5tab: Crystal Structure of the PHD Finger of PHF20 -

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Basic information

Entry
Database: PDB / ID: 5tab
TitleCrystal Structure of the PHD Finger of PHF20
ComponentsPHD finger protein 20
KeywordsTRANSCRIPTION / PHD Finger
Function / homology
Function and homology information


NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / chromatin organization / HATs acetylate histones / nuclear membrane ...NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / chromatin organization / HATs acetylate histones / nuclear membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsKlein, B.J. / Kutateladze, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100907, GM106416, GM101664 United States
CitationJournal: Cell Rep / Year: 2016
Title: PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation.
Authors: Klein, B.J. / Wang, X. / Cui, G. / Yuan, C. / Botuyan, M.V. / Lin, K. / Lu, Y. / Wang, X. / Zhao, Y. / Bruns, C.J. / Mer, G. / Shi, X. / Kutateladze, T.G.
History
DepositionSep 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3144
Polymers6,0911
Non-polymers2233
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area3930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.739, 46.739, 50.928
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PHD finger protein 20 / Glioma-expressed antigen 2 / Hepatocellular carcinoma-associated antigen 58 / Novel zinc finger ...Glioma-expressed antigen 2 / Hepatocellular carcinoma-associated antigen 58 / Novel zinc finger protein / Transcription factor TZP


Mass: 6090.889 Da / Num. of mol.: 1 / Fragment: residues 651-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20, C20orf104, GLEA2, HCA58, NZF, TZP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rossetta2 / Variant (production host): RIPL / References: UniProt: Q9BVI0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M bis-tris propanol pH 6.5, 2.55 M ammonium sulfate titrated with 0.006 ml per 1 ml 1 N HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→31.69 Å / Num. obs: 33909 / % possible obs: 99.7 % / Redundancy: 1.9 % / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692model building
RefinementMethod to determine structure: SAD / Resolution: 1.25→31.688 Å / SU ML: 0.09 / Cross valid method: NONE / σ(F): 0 / Phase error: 12.59
RfactorNum. reflection% reflection
Rfree0.1435 1641 9.47 %
Rwork0.1182 --
obs0.1206 17326 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→31.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms418 0 8 71 497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012443
X-RAY DIFFRACTIONf_angle_d1.472597
X-RAY DIFFRACTIONf_dihedral_angle_d17.959166
X-RAY DIFFRACTIONf_chiral_restr0.07663
X-RAY DIFFRACTIONf_plane_restr0.00979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28680.21671300.17521246X-RAY DIFFRACTION94
1.2868-1.32840.20481330.15611280X-RAY DIFFRACTION97
1.3284-1.37580.1561350.12861278X-RAY DIFFRACTION98
1.3758-1.43090.14261310.10831282X-RAY DIFFRACTION99
1.4309-1.4960.12841420.09681320X-RAY DIFFRACTION99
1.496-1.57490.11581370.09231311X-RAY DIFFRACTION100
1.5749-1.67360.12311370.09491321X-RAY DIFFRACTION100
1.6736-1.80280.12331360.0971327X-RAY DIFFRACTION100
1.8028-1.98420.13461420.11151295X-RAY DIFFRACTION100
1.9842-2.27120.14711360.12341334X-RAY DIFFRACTION100
2.2712-2.86120.15731390.131333X-RAY DIFFRACTION100
2.8612-31.69790.13851430.12111358X-RAY DIFFRACTION100

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