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- PDB-5b79: Crystal structure of DPF2 double PHD finger -

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Basic information

Entry
Database: PDB / ID: 5b79
TitleCrystal structure of DPF2 double PHD finger
ComponentsZinc finger protein ubi-d4
KeywordsMETAL BINDING PROTEIN / DPF2
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / histone H3K14ac reader activity / histone H4K16ac reader activity / histone H3K9me2/3 reader activity / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair ...negative regulation of myeloid progenitor cell differentiation / histone H3K14ac reader activity / histone H4K16ac reader activity / histone H3K9me2/3 reader activity / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / : / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / apoptotic signaling pathway / transcription corepressor activity / nervous system development / chromatin remodeling / intracellular membrane-bounded organelle / apoptotic process / centrosome / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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
Zinc finger protein ubi-d4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsLi, H. / Xiong, X.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2
Authors: Xiong, X. / Panchenko, T. / Yang, S. / Zhao, S. / Yan, P. / Zhang, W. / Xie, W. / Li, Y. / Zhao, Y. / Allis, C.D. / Li, H.
History
DepositionJun 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Zinc finger protein ubi-d4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0805
Polymers13,8191
Non-polymers2624
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7600 Å2
Unit cell
Length a, b, c (Å)106.979, 106.979, 52.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Zinc finger protein ubi-d4


Mass: 13818.602 Da / Num. of mol.: 1 / Fragment: UNP residues 270-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92785
#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.: 10 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: ammonium citrate tribasic, Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→23.6 Å / Num. obs: 4902 / % possible obs: 99.6 % / Redundancy: 7.5 % / Net I/σ(I): 29.9
Reflection shellResolution: 2.6→2.64 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data processing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LLB

4llb


Resolution: 2.601→23.599 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.68
RfactorNum. reflection% reflection
Rfree0.238 476 9.71 %
Rwork0.1894 --
obs0.1941 4902 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.601→23.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 4 10 928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006934
X-RAY DIFFRACTIONf_angle_d0.941261
X-RAY DIFFRACTIONf_dihedral_angle_d15.662570
X-RAY DIFFRACTIONf_chiral_restr0.044133
X-RAY DIFFRACTIONf_plane_restr0.004165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6015-2.97730.34681370.28231467X-RAY DIFFRACTION100
2.9773-3.74860.27581590.20841445X-RAY DIFFRACTION100
3.7486-23.59950.19081800.15231514X-RAY DIFFRACTION99

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