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- PDB-7duf: Crystal structure of VIM1 PHD finger. -

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Basic information

Entry
Database: PDB / ID: 7duf
TitleCrystal structure of VIM1 PHD finger.
ComponentsE3 ubiquitin-protein ligase ORTHRUS 2
KeywordsLIGASE / ORTHRUS 2 / plant homeodomain / Zinc finger / Arabidopsis / PHD finger
Function / homology
Function and homology information


: / : / : / methyl-CpNpG binding / methyl-CpNpN binding / positive regulation of DNA methylation-dependent heterochromatin formation / chromocenter / double-stranded methylated DNA binding / pericentric heterochromatin formation / methyl-CpG binding ...: / : / : / methyl-CpNpG binding / methyl-CpNpN binding / positive regulation of DNA methylation-dependent heterochromatin formation / chromocenter / double-stranded methylated DNA binding / pericentric heterochromatin formation / methyl-CpG binding / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / protein ubiquitination / cell division / chromatin binding / metal ion binding / nucleus
Similarity search - Function
SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / PUA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / PUA-like superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ORTHRUS 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsAbhishek, S. / Deeksha, W. / Patel, D.J. / Rajakumara, E.
CitationJournal: Biochemistry / Year: 2021
Title: Helical and beta-Turn Conformations in the Peptide Recognition Regions of the VIM1 PHD Finger Abrogate H3K4 Peptide Recognition.
Authors: Abhishek, S. / Deeksha, W. / Rajakumara, E.
History
DepositionJan 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ORTHRUS 2
B: E3 ubiquitin-protein ligase ORTHRUS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4786
Polymers14,2162
Non-polymers2624
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-11 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.590, 74.590, 58.880
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

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Components

#1: Protein E3 ubiquitin-protein ligase ORTHRUS 2 / Protein VARIANT IN METHYLATION 1 / RING-type E3 ubiquitin transferase ORTHRUS 2


Mass: 7108.122 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ORTH2, VIM1, At1g57820, F12K22.14 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: Q8VYZ0, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.28266 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28266 Å / Relative weight: 1
ReflectionResolution: 2.61→32.3 Å / Num. obs: 11062 / % possible obs: 98.89 % / Redundancy: 10.3 % / Biso Wilson estimate: 76.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07882 / Net I/σ(I): 25.77
Reflection shellResolution: 2.61→2.7 Å / Rmerge(I) obs: 0.6623 / Mean I/σ(I) obs: 3.53 / Num. unique obs: 599 / CC1/2: 0.971 / % possible all: 98.34

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: SAD / Resolution: 2.61→32.3 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.4214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 561 5.07 %
Rwork0.2149 10501 -
obs0.2157 11062 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.37 Å2
Refinement stepCycle: LAST / Resolution: 2.61→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms836 0 4 7 847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023862
X-RAY DIFFRACTIONf_angle_d0.59081188
X-RAY DIFFRACTIONf_chiral_restr0.0371139
X-RAY DIFFRACTIONf_plane_restr0.0056153
X-RAY DIFFRACTIONf_dihedral_angle_d4.9786118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.870.38251420.37612586X-RAY DIFFRACTION96.23
2.87-3.280.34571440.32382640X-RAY DIFFRACTION99.71
3.28-4.130.25511390.22152654X-RAY DIFFRACTION99.15
4.13-32.30.18371360.16882621X-RAY DIFFRACTION98.78

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